There was a thread EXACTLY like this not a few days ago as well.
Part 1: Why should you do this?
Many people say that if you just want a manual transmission, sell your automatic and buy a manual. It is probably not worth the effort or money if you're JUST looking for a manual transmission.
However, if your car is paid off, un-sellable (hail damage, like mine is, for example), or you also want to learn and gain experience working on Subarus, why not?
Basically there are two ways to do this: The easy/cheap way, or the thorough/expensive way.
The easy way is less expensive and keeps your 4EAT ECU, TCU, and ABS unit, but you lose cruise control, might get a CEL, and need a tune for the 5MT throttle tables.
The thorough way involves swapping to a 5MT ECU and swapping the wiring harness, plus the 5MT ABS unit. Read: time-consuming and expensive, but you keep all factory features and have a car that is exactly like a 5MT from the factory. This gives you the penultimate "clean-all-under" feeling.
For the basic, cheap & easy 5MT swap you need:
-5MT + matching ratio rear diff
-5MT driveshaft
-full shifter linkage + clutch fork + all assorted nuts and bolts
-slave cylinder assembly
-5MT starter
-5MT tranny crossmember and tranny mount (according to amorgan, you need a Forester specific tranny crossmember- never heard that before but could be)
-5MT shifter gate trim (the AT trim is slightly smaller than the 5MT trim and is too small for the stock 5MT shifter, but if you go with an aftermarket short shifter you don't need the 5MT trim)
-clutch pedal assembly (make sure pull or push style clutches and stuff all match up)
-front and rear axles, make sure the male and female match up- some years were male and others female
-clutch/pressure plate
- wiring to make it all work (I will address later)
For the "thorough" version of the 5MT swap you must add:
-5MT ABS unit
-full 5MT wiring harness
-5MT ECU
-probably something else I forgot to mention
As for the procedure:
The mechanicals are all there in the chassis, but the wiring is probably the hardest part.
You need to:
1. Merge 5MT speed sensor wires so that your speedometer works. If you don't do this your speedometer won't work, and your engine will be limited to 4000 RPM and set off a VSS CEL.
2. Merge a reverse lamp connection otherwise reverse lamps won't work when your car is in reverse. The car will run fine without doing this, but it is a safety issue to not have reverse lamps illuminated when backing up, so consider this a must-do as well.
3. Ground pin on 4EAT ECU to tell ECU that it's a 5MT. I forgot what exact pin this is but a Nasioc search should give some results.
4. Wire up clutch depression switch so the car won't start unless the clutch pedal is pressed. Not necessary for the car to work, but you don't want to start your car when it's in gear so this might be a good one if you tend to forget to press in the clutch before you start the car. You might as well do this if you're going to the trouble of a 5MT swap.
5. Close neutral safety switch for AT so you can start vehicle. On the 4EAT, there is a momentary switch in the P and N positions of the shifter gate that closes a circuit when the shifter is in P or N. When the shifter is not in P or N and the circuit is open, your car will not start. Permanently close this circuit so your 4EAT ECU will always think the bygone 4EAT is in P or N and there will be no troubles starting your car. Simple as soldering two wires together.
6. Jump the ignition key release so your car will not trap your key in the ignition switch. Simple as soldering two wires together.
7. Splice into ignition wires going to the 5MT starter.
8. Open source tune for 5MT fuel maps. At idle, the 4EAT ECU puts a little more gas in to keep from stalling from the resistance of the torque converter. When idling in the 5MT cars, the clutch is not engaged and no resistance from a torque converter. A high idle would get annoying.
9. If you remove the 4EAT TCU, you will lose ABS. Simple- you keep the 4EAT TCU. Yes it can be done with a 5MT swap, you don't have to remove your old TCU.
Good reads:
DIY Auto to Manual Swap
2005 WRX-98 LGT wagon 5MT swap
Parts list for a PROPER 4EAT to 5MT swap?
Best source out of all of them:
Converting your 4EAT to 5MT <-- This is a great read. Read it once, read it twice, read it three times.
By the way, it's not always as costly $2500+ as many people think. If you do the labor yourself, this swap could be done for under $1500 and you can sell some of your old parts. I've seen 5MT on Nasioc go for under $1000 with less than 100K miles. And for the people who are doing a 5MT--> 6MT swap, a 4EAT driveshaft is needed, so you can make a lot of $$$ off selling your old auto driveshaft. The 4EATs themselves don't sell well though; you probably won't get over $250-$300 for a 4EAT. No one needs an auto tranny because they are pretty tough and no one wants to do a manual --> auto swap.
As an added bonus with the 4EAT--> 5MT swap, there is a lot more room in the auto tranny tunnel for the big 4EAT, so installing the new 5MT should be easier in a wide-open space. Also, the 5MT weighs a LOT less than the 4EAT, so you have some weight reduction there. As if that wasn't enough, the power-hogging auto is gone and you should have a noticeable increase in power because of less driveline drag.
**If I've said anything wrong, please correct me.