[Guest]

This thread is all about the 5MT swap. My swap was done on an '06 SG9, but all the part numbers I've listed will fit any SG Forester and should be cross-compatible with SF models too. SH and SJ owners be aware of possible compatibility issues, as I don't know anything about them.


Part 1: Why?

So why would you do this? For starters, I don't recommend doing this swap if you ONLY want a manual and don't enjoy working on your car. Sell your Forester and buy a 5MT version and save yourself the headache of doing the swap and correcting the following electrical issues. If you have an unsellable Forester (like mine with hail damage and salvage title) or have a bunch of mods in yours that you don't want to lose, carry on:

You should do this swap if:

1. You want a manual transmission and your Forester is unsellable or you have too many mods into it to resell

2. You enjoy working on cars

3. You can allot at least a week for installing all the parts

4. You have saved double your intended budget

5. You don't plan to ever resell your car (non matching trans code means that the swap destroys your resale value)

6. You are prepared to do or have done hundreds of hours of research. This thread is a good start, but here are some other good threads: Basic parts list, the two basic swap options, more thorough parts list ('05 WRX), overview of electrical problems to sort out, Legacy 5MT swap journal.

7. You're not afraid to get your hands dirty

8. Your car is out of warranty- this will certainly void your warranty and dealerships might refuse to work on your car

Parts needed will be covered in the next post.

 

[Guest]

Parts List

Part 2: Parts, Tools, & Materials

Here is an overview of the parts you need. Make sure what you're doing is cross-compatible with your Forester model. Things like the 5MT transmission crossmember are Forester-specific due to the subframe spacers that the Impreza does not have. Remember axle compatibility and push/pull style clutch years. Impreza 5MTs are much more readily available than Forester 5MTs because Foresters have shorter gear ratios (4.11 and 4.44), so this write-up is geared towards swapping an Impreza transmission. I swapped a 3.90 in mine from an '04 WRX, but shortly blew the main shaft out- be careful buying used transmissions!

Mechanically, everything is a direct bolt-in. Subarus are like Legos and a lot of parts are cross-compatible between different years and car models.

Basic Parts List:

1. Transmission
2. Matching ratio rear diff
3. 5MT driveshaft (4EAT/6MT driveshaft is too long)
4. Matching front axles- for the Impreza, '02-early '04 axles were female and '04-'07 axles were male.
5. Clutch/flywheel/pressure plate- clutch system must match if you have a push or pull style clutch. I sprang for an XTD Stage 3 six-puck clutch and matching pressure plate. It sucked. I replaced it with an organic clutch.
6. Clutch master/slave cylinders and clutch lines- make sure slave cylinder is for your push/pull style clutch system.
7. 5MT pedal box- anything from '02-'07 Impreza or Forester will work. I used a pedal box from an '04 which has fancy silver pedal pads. The accelerator pedal is completely separate from the clutch/brake pedal box so don't worry about DBW compatibility.
8. 5MT shifter assembly (make sure you get the right wide vs narrow shifter)- shifter assembly includes shifter and shift knob, rubber gasket, pivot bushing and bolts, lower shifter ball bushing and rear shifter bushing/bracket assembly, and the other half of the shifter assembly (sometimes left attached to the trans). This is a good time to upgrade to an aftermarket short shifter since the stock Forester shifter is so tall! This is also a good time to upgrade all your shifter bushings.
9. Trans mount (good time to upgrade to Group N)
10. Forester-specific 5MT transmission crossmember- good time to upgrade to stiffer crossmember bushings
11. Forester-specific interior shifter trim & shift boot
12. 5MT starter- the starter bolts onto the bell housing of the trans and is different for 4EAT and 5MT vehicles.

The easiest method of obtaining these parts is buying a used "transmission swap" package deal from an Impreza owner who is doing an STi 6MT swap. These package deals normally include the trans, rear diff, driveshaft, axles, and starter and will run you anywhere from $800-$1500 depending on year and mileage. This way, you know all of the drivetrain parts are from the same car with the same amount of mileage in the same condition. Avoid the '02 5MT because it had weak gears. I suggest finding the lowest mileage 5MT you can from a stock car that doesn't have performance mods putting more torque on the transmission. I bought an '04 WRX 5MT swap package, but little did I know the transmission had a bad main shaft rear brake plate. Be careful buying used transmissions.


The following section is where things deviate. If you want to get rid of everything 4EAT, you'll remove the TCU which is also the ABS controller on *some* 4EAT vehicles. On my vehicle, removing the TCU did NOT remove ABS. For some vehicles, you'll need a 5MT wiring harness and 5MT ABS unit if you want to do this whole swap. It also eliminates some other electrical issues which will be discussed later.

More specific parts list:

1. 4EAT flex plate bolts are too short to serve as flywheel bolts. The part number for the flywheel bolts is 800610740 and you need 8 of them.
2. Extra bolt for the 5MT clutch/brake pedal box that bolts up under the dash. The tapped hole is already there with an inserted plastic plug. The bolt is part number 901000267.
3. Extra clevis pin & spring pin for the clutch pedal linkage, part numbers 736016020 and 051108001.
4. Two flange nuts for where the master cylinder connects to the clutch pedal box linkage through the firewall, part number 023808000.
5. Bolts for attaching the pressure plate to the flywheel, part number 800508310 and you need 6 of them at least for the '02 flywheel. '02-'04 are identical but I can't speak for '05+.
6. You'll probably want to press a new pilot bearing into a used flywheel. The pilot bearing is part number 806212020.
7. You also might want to replace the rear main seal while the output shaft of your engine is exposed. Rear main seal for the EJ253 is part number 806786040.
8. The transmission axle seals probably need replacing. I can't find the part number for this one.
9. The rear differential axle seals also probably need replacing. The part number for the '03+ Impreza rear diff axle seals is 806735240 and you need 2 of them.

I'm sure I'm missing some random nuts and bolts so feel free to chime in. You reuse your 4EAT bell housing bolts and some of the bolts from the 4EAT transmission crossmember and mount. Your used crossmember, mounts, and other small parts should come with the attaching bolts, ask your parts seller.

Tools:

I was fortunate that my uncle lent me access to a hydraulic lift, air power, and a variety of quality Matco tools and impact sockets as well as all kinds of wrenches. An electric impact wrench made undoing tight bolts a lot quicker than the breaker bar, but even the impact wrench couldn't undo that long lateral link bolt. :icon_eek: We had to pull out the breaker bar for that one.

The following tools are absolutely necessary, in my opinion:

1. Breaker bar
2. 32mm socket for undoing axle nuts
3. Ball joint puller tool
4. 50-150ft/lbs torque wrench
5. High quality or impact socket set
6. Torx T-70 bit for undoing the transmission drain plug
7. Bit for undoing the rear diff drain plug. I used the 1/2" breaker bar socket and didn't have any problems, but the specific plug fits better and you don't risk munting the plug.
8. Hydraulic lift really makes things so much easier. There was no way I would have been able to swap the mechanical parts in less than a week without the lift. I HIGHLY recommend you find some way to get access to one of these for 7 days or so.
9. Gloves (sort of optional); I say sort of optional because I don't like working with gloves to retain the bare-handed touch sense, but I wore gloves when working around the sharp exhaust heat shields and while pulling the engine and transmission.
10. Safety glasses for protecting your eyes from falling dirt.
11. Oil catch pan for catching dripping ATF- when you pull the trans, ATF will pour out of the 4EAT tail shaft as well as the ATF cooler lines.
12. Steel-toed boots; optional but extra insurance in case you drop something heavy, which I nearly did a few times with slippery fluids on my hands. A torque converter with the starter gear-toothed edge doesn't feel so good when you drop it on your foot.


Materials:

1. 75W-90 gear oil, without limited slip modifiers because the 5MT doesn't like the modifiers.
2. Anti-seize compound.
3. Tape and a permanent marker for labeling engine compartment wires.
4. Waterproof grease for installing the axles. Those are a big pain to remove, one was so stuck in the hub I had to cut the axle in half and take the hub to the shop to get the stub pressed out.
5. Tons of shop rags for soaking up spilled ATF and oil. An ATF-soaked rag wrapped around a stick makes a great torch. :biggrin:
6. Mineral spirits for cleaning up parts
7. Fast Orange or other pumice hand cleaner for getting grease off your hands
8. Clothes you don't care about getting oil and grease all over

 

[Guest]

Part 3: Possible Problems, Tips, & Techniques


Mechanical Problems

There are a few known mechanical issues to sort with the swap, otherwise everything is a direct bolt-in. The 4EAT and 5MT vehicles share the same chassis, so all the tapped holes and spot-welded nuts are there, but many of them have removable plastic plugs in them that keep the threads clear of dirt and weathering.

Be aware of the following:

1. Front axles must match for male/female years.
2. Clutch manipulation systems must match your push or pull style transmission. Any year '02-'07 clutch/brake pedal box will work with both push and pull style clutch systems.
3. Due to the Impreza's lack of the Forester subframe spacers, an Impreza rear diff is shorter in height than a Forester rear diff. An aluminum spacer would be the best solution; I made up the difference with washers. :biggrin:
4. The rear diff ratio must match the transmission, for the same reason you must have matching tires. The difference will destroy your center diff if they don't have the same ratio.
5. You must get the Forester-specific 5MT transmission crossmember, due to the Forester's subframe spacers. The transmission mount does NOT have to be Forester-specific- I took the liberty of upgrading to a Group N mount.


Electrical Problems:

1. For some model years, if you remove the TCU, you lose ABS because the TCU also serves as the ABS controller. Solution: don't remove the TCU or get a 5MT wiring harness and 5MT ABS unit. My '06 does NOT have this problem. Removing the TCU did not affect ABS functioning.
2. Speedometer- the 4EAT has 3 speed sensors- one for the torque converter, one for the front gearset, and one for the MPT clutch in the center diff. The 5MT only has one speed sensor with 3 output pins. If you don't have a speed signal coming from the sensors, you will throw a P0502 CEL for VSS fault and will be stuck in limp mode (stuck in open loop which kills your gas mileage) with a 4000 RPM rev limit, and will also have no speedometer. See solution below or the edit. Previous speculation suggested that a 4EAT speed sensor would be a direct swap into a 5MT, but it is NOT. Newer 4EATs have a harness with 3 magnetic speed sensors (one for the torque converter, one for the front gears, and one for the MPT clutch) that isn't even close to a direct bolt in. I still haven't figured out how to get the 3-pin 5MT speed sensor to work with the 4EAT bulkhead harness, so I have a rev limit, no speedo, and less than 20 MPG. I'm ending up just deleting the CEL with a Tactrix box and removing the rev limit and going without a speedometer.
3. Reverse lights, since you won't have the AT shifter to tell the car it's in reverse, the car has no idea what whether you are in reverse or 1-5. Solution: hook up "reverse" pins from the AT inhibitor switch diagram to the reverse switch on the transmission.
4. Starter won't turn when you turn the key because the starter is hooked up for the 4EAT. Solution: run the "P" position pins from the AT inhibitor switch to the clutch pedal so you have to push the clutch to start the car. When the clutch is out, your car will go into closed loop like it's driving, when you press in the clutch, the car will go into open loop like it's idling.
5. Ignition key interlock system will trap your key in the ignition because it thinks you're not in P. Solution- jump the ignition key interlock system which is on the top of the 4EAT gear selector unit.
6. Contrary to popular belief, at least for '05+ there is NO pin you have to ground on the ECU to tell the ECU your car is a manual now.
7. Possible idle issues- the ECU makes idle in D a bit higher for the 4EAT vehicles because it should have been fighting against the resistance of the torque converter, but now that there is no torque converter there is less resistance and idle is a bit higher. When I cold start the car idle will shoot up to 2000 RPM for a minute or two. You can tune this out with a Tactrix cable.
8. ATF temp sensor missing from the sensor circuit sends "ATF too hot" signal to the ECU so radiator fans run at full blast all the time. I haven't seen this one mentioned in a 5MT swap thread yet. Jump the ATF temp sensor circuit with a resistor to fool the circuit into thinking the ATF temp is safe. I'm not sure what the resistance value is for "safe operating temp" but I'm sure the factory service manual mentions it.


***EDIT 12-1-2014:***

User "TallazzPilipino" has written an excellent, thorough write-up with specific harness and TCU plug pin numbers about wiring these up while deleting the TCU. Keep in mind his swap was done on an SG5, so some pin numbers may differ between VDC 4EATs. Here is the link to that post: http://www.subaruforester.org/vbulletin/f89/how-wire-your-4eat-5mt-swap-414786/


Tips & Techniques

1. Check over all the parts you have for compatibility! I ordered the wrong throw-out bearing and had to spend $200 markup price at the local Subaru dealership for the correct pull-style throw-out bearing
2. Know your transmission seller. I bought a borked transmission and blew the main shaft within a month, which led to me spending a few thousand dollars to get a brand new transmission installed.
3. Plan for extra time on things you don't expect, like having to saw a stuck axle and pressing the stub out of the wheel hub.
4. Save at least double your intended budget. I certainly didn't plan to spend a few thousand dollars on a new transmission. You never know what will pop up.
5. Double and triple check your part numbers before ordering.
6. Double and triple check your parts pile before beginning the swap. I traveled out of town for my swap and had to either rush parts from a Subaru parts website or spend 200% markup at the local Subaru dealership if I forgot something.
7. Do as much as you can before having to rent the hydraulic lift or garage. I installed the brake/clutch pedal box a month before officially starting my swap, but that's about all you can do before really getting your hands dirty and dropping the 4EAT.
8. Arrange for resale of your old parts or have some place to store them before beginning your swap. All the old parts really take up space, and the 4EAT doesn't sell very well since it's so tough and nobody is breaking them. I'll probably end up selling mine as a core charge or to a metal scrap yard for $1/lb if no one buys mine ($150 OBO takes it :biggrin. The 4EAT driveshaft sells well around $75-80 as people use them for 6MT swaps. The 4.44 rear diff also sells well for around $120. Other parts such as the 4EAT shifter selector assembly and auto brake pedal box don't sell as well since no one needs replacements- they're not maintenance items after all.

 

[Guest]

The Process

Keep in mind, I used a hydraulic drive-on lift and also pulled my engine to change the timing belt + components and head gaskets. If you pull the motor you don't need to remove the hood, bumper, head lamps, or quarter panels like I did. I also had to run intercooler piping for my supercharger project, which I'll do a lengthy write-up on as well.

1. Install the clutch/brake pedal box. I did this before I even officially began my swap, and it's easier to do this when a lift isn't in your way. I spent about 1.5 hours laying on the ground contorted under the dash installing it. Contrary to popular belief, you do NOT have to pull the steering column or anything drastic like that, just move the steering wheel to the tallest possible setting and lock it. My write-up for installing the clutch/brake pedal box is here: 5MT Brake/Clutch Pedal Box Install. I used an '04 WRX assembly which has the Sports silver pedal pads, but anything '02-'07 WRX should be a direct bolt-in. You'll need that extra flange bolt to install it, part number 901000267. The threaded hole is already there, but there is a plastic plug that you have to pry out to access the hole. Throughout the process you'll encounter the plastic plugs, which are good because they keep the threads clean.

2. Lay all your parts out and get the car up on the lift. This is the last time you'll ever use the 4EAT...

3. Remove all 4 tires. Since my lift was a drive-on lift, I put it on jack stands on the lift, then removed the tires.

4. Drain the ATF and rear diff. Remember there will be ATF left in the cooler lines running to the built-in ATF cooler in the radiator.

5. Drop the driveshaft. Undo the 4 bolts attaching it to the rear diff input shaft, then undo the 2 carrier bearing bracket bolts. When you pull the front of the driveshaft out of the tail of the transmission, some ATF will come out so have a rag ready.

6. Drop the rear diff. This requires unbolting the bottom bracket of the rear diff carrier, undoing one of the rear hubs and undoing one of the lateral link bolts (bust out the breaker bar for this one) and endlinks, then undoing the 4 nuts under the rear diff and pulling the whole assembly out of the outrigger bushings. Be careful, it's heavy. I still had the wheels on and rear hubs connected (I undid them when installing the new R160) at this point.

7. Undo the rear hubs if you haven't already done so by undoing the lateral link bolt. This bolt is torqued to 150ft/lbs and required a breaker bar and cheater pipe to remove, not even the impact wrench would remove it. Cheap sockets probably would have split, but we I had Matco impact sockets at my disposal. Then remove the axles by wedging between the green part of the axle and the rear diff body and prying them apart. I pressed the axles out of the wheel hub with a spline bit and a heavy mallet. You shouldn't have to buy rear axles, they should be identical- at least mine were between '04 WRX and my '06 Forester.

8. Reinstall the new R160 in reverse order of the previous 2 steps. This was the space difference between the Forester and the Impreza rear diff:

9. Undo the front hubs by unbolting from the struts, unbolting the front endlinks, unbolting the brake calipers, and unbolting the ball joints. Removing the ball joints was a pain, and a ball joint puller tool is invaluable. Then, knock the axle out of the hub.

10. Pull the axles out of the trans using the same method you used to pull the axles from the rear diff.

11. Now begins dropping the transmission. I pulled the engine to remove everything since I was working on the engine anyway. Basically, you have to disconnect the shifter assembly and wiring harness from the 4EAT. First, support the transmission with a transmission jack and undo the trans crossmember and mount. Undo the shifter linkage and unplug the two wiring harness plugs connecting near the bell housing of the transmission.

12. At this point I recommend unbolting the engine mounts and tilting the engine backwards (requiring disassembling the TMIC or other intake system) to undo the bell housing bolts and gently removing the transmission. Note: I HIGHLY recommend pulling the engine! The 4EAT and its torque converter are heavy, and the torque converter leaks a bunch of ATF.

13. I pulled my engine with the 4EAT attached- once all the engine bay wires and hoses were disconnected it only took 15 minutes to maneuver the big 4EAT out of the engine bay.

 

[Guest]

The Process (cont.)

The Process (cont.)


14. Once you have the 4EAT on the table you can unbolt the torque converter from the flex plate by fitting an open-end wrench between the torque converter and the rear of the engine. As I mentioned before, the torque converter holds quite a lot of ATF.

Flex plate:

15. You can also pull the interior shifter trim and the 4EAT shifter selector assembly, you won't be needing that anymore. Go ahead and jump the ignition key interlock toggle switch on the top of the selector assembly while you're in there, it's the easiest part of the electrical work.

16. Install your flywheel with the 8 new flywheel bolts and install the clutch and pressure plate. Be sure to use a clutch alignment tool.

17. Mate the new transmission to the engine. Do NOT, I repeat, DO NOT use the bell housing bolts to "pull" the engine and trans together!! If the clutch is misaligned you could bend the main shaft brake plate doing this, leading to popping out of gear and eventually walking the main shaft and destroying your transmission. Push the engine and transmission together correctly and the bell housing bolts should go in smoothly. Install the 5MT-specific starter as well.

18. Reinstall the transmission/engine (if you pulled the engine like I did) using the Forester-specific transmission crossmember.

19. Install the 5MT shifter assembly, the rear shifter stay bushing holes have plastic plugs in them but they are threaded so the rear shifter stay is a direct bolt in. This would be a great time to upgrade to stiffer bushings! Contrary to popular belief, the throw of the stock shifter does not require 5MT-specific shifter trim, it just looks ugly if you don't have a shift boot.

20. Install the 5MT driveshaft.

21. Run the starter pins on the AT inhibitor harness to the clutch switch under the dash and test fire! If it starts it should work, but you can resolve the speed sensor issues later if need be.

 

[Loscaldazar]

This is where things deviate. If you want to get rid of everything 4EAT, you'll remove the TCU which is also the ABS controller on 4EAT vehicles. You'll need a 5MT wiring harness and 5MT ABS unit if you want to do this.

IF you want ABS.... :evilatyou:

Looking forward to the entire write up!

 

[pleiad7]

Stickied!

 

[Guest]

Stickied!

I have reached the 2nd tier of online forum fame- getting a post stickied. :biggrin: Now all that's left is a custom user title. :biggrin:


Finished write-ups for Parts 1, 2, and 3. Now onto Part 4: the process. :icon_eek: Lots of pictures and details for this one, will probably take up the last 2 reserved posts.

 

[CinderBlock]

You are the man Mr. Golfball!

This is epic.

Sent from AutoGuide.com Free App

 

[jpegone]

Oh, how I wish I would be using this. Great thread though.

Sent from my Nexus 4

 

[Amber Foresty]

I can't wait to read this! Haha I'd never do it myself, probably, (plus my Forester is already manual), but will be interesting to see how it's done, step-by-step.

So you said you're going without a speedometer, huh? Does that mean you'll have no indication of your speed at all (or am I just an idiot)?

 

[Guest]

So you said you're going without a speedometer, huh? Does that mean you'll have no indication of your speed at all (or am I just an idiot)?

No solid indication from the speedometer which stays at 0, but I know *about* how fast I'm going based on the engine RPM and what gear I'm in. For instance, 2000 RPM in 4th gear is about 33 MPH or so. Or, I just go with the flow of traffic.

Now onto the process section. Fingers are warming up...

 

[Amber Foresty]

No solid indication from the speedometer which stays at 0, but I know *about* how fast I'm going based on the engine RPM and what gear I'm in. For instance, 2000 RPM in 4th gear is about 33 MPH or so. Or, I just go with the flow of traffic.

Now onto the process section. Fingers are warming up...

Wow, that's actually kind of how I drive too lmao so I can't believe I didn't think of that! Now that I know the speeds of my engine (well, not really at highway speeds, because I don't travel in fifth gear all that often), I can really just look at either gauge and figure out how fast I'm going in kilometres. :biggrin:

Personally, I think what you're doing is much cooler than driving with a speedometer, although I don't particularly want to ruin mine.

 

[Guest]

Whew, I think I'm done. Let me know with any suggestions or corrections or if there's something you want me to go into more detail about.

 

[CinderBlock]

Thanks man! I doubt I'll ever use this info myself, but it is awesome to have it available!

 

[Amber Foresty]

Whoo! Awesome guide! I need to go term-hunting though as I didn't always understand everything... haha.

"Diff" is the differentials, right? Had no idea those had anything to do with the transmission...

 

[Guest]

Diff is shorthand for differential. There are three diffs in the AWD system- front diff which distributes power between the two front wheels, center diff which distributes power between the front and rear drives, like how the 4EAT multi-plate transfer clutch normally distributes around 70% to the front and 30% to the back but locks to 50% front and 50% rear when it detects wheel slip, and rear diff which distributes power between two rear wheels.

 

[AJ711]

Part 1: Why?

So why would you do this? For starters, I don't recommend doing this swap if you ONLY want a manual and don't enjoy working on your car. Sell your Forester and buy a 5MT version and save yourself the headache of doing the swap and correcting the following electrical issues. If you have an unsellable Forester (like mine with hail damage and salvage title) or have a bunch of mods in yours that you don't want to lose, carry on:

You should do this swap if:

1. You want a manual transmission and your Forester is unsellable or you have too many mods into it to resell

2. You enjoy working on cars

3. You can allot at least a week for installing all the parts

4. You have saved double your intended budget

5. You don't plan to ever resell your car (non matching trans code means that the swap destroys your resale value)

6. You are prepared to do or have done hundreds of hours of research. This thread is a good start, but here are some other good threads: Basic parts list, the two basic swap options, more thorough parts list ('05 WRX), overview of electrical problems to sort out, Legacy 5MT swap journal.

7. You're not afraid to get your hands dirty

8. Your car is out of warranty- this will certainly void your warranty and dealerships might refuse to work on your car

Hit. Every. Reason. Perfectly.

I completed this same project on my RS not too long ago. Did it myself, it took a number of weeks of after work/weekend hours spent in the garage swearing at things, I ran into a few problems, but all in all, it went smoothly.

I still have some wiring work to iron out, but the car has made a number of long'ish trips with zero issues. I'll post up some thoughts and findings from my work once I'm home and have had a chance to collect my thoughts.

Excellent post and photos.



As for the speedometer, swap your speed sensor over from the automatic transmission to the 5MT. There are ways of hacking the wiring up to utilize the 3-wire 5MT speed sensor, but it is also easier to just swap the two parts out. I did this and the speedometer works perfectly.

 

[Guest]

I still have some wiring work to iron out, but the car has made a number of long'ish trips with zero issues. I'll post up some thoughts and findings from my work once I'm home and have had a chance to collect my thoughts.

The 800 mile drive home with no speedometer and a block of wood serving for the transmission mount (my Group N mount hadn't come in yet) and popping out of 4th gear from my blow main shaft brake plate was sort of scary. :icon_eek: :lol:

As for the speedometer, swap your speed sensor over from the automatic transmission to the 5MT. There are ways of hacking the wiring up to utilize the 3-wire 5MT speed sensor, but it is also easier to just swap the two parts out. I did this and the speedometer works perfectly.

I don't know about the older models, but my 4EAT has 3 magnetic speed sensors (one for torque converter, one for front gearset, one for MPT clutch) that are completely different from the geared 5MT speed sensor. Can you post a pic of those speed sensors?

I took a pic comparing the speed sensors; 5MT on left, 4EAT front sensor on right:

Even at first glance, the 5MT 3-wire sensor is much bigger in size and has a threaded neck for screwing it into the transmission case.

 

[AJ711]

I don't have a picture of the speed sensors, but I will agree with the 4EAT having 3. There are two on the driver's side of the case, and those are not necessary. The 3rd is on the passenger side and looks similar to the 5MT one.

I went from a MY98 4EAT to a MY97 5MT, so things were relatively the same. I did end up ordering a new 4EAT speed sensor, as removing the original was a PITA, and I ended up having to rip out the 5MT sensor.

Here is a stock image of a 2 wire speed sensor.

http://cdn2.autopartsnetwork.com/images/catalog/wp/full/W01331822062OES.JPG

The basic jist of it is, there will be a piece that looks similar to your 5MT sensor in the 4EAT. Remove that piece, or purchase a new unit, and swap it in place of the 3 wire sensor on the 5MT case. The ECU is looking for a specific signal provided by the speed sensor. Since you're basically keeping the ECU the same, it is just easier to keep the speed sensor and lower the possibility of signals being mixed up.