so, you've completed the mechanical part of your 4eat to 5mt swap and are stumped with the wiring. well, you've come to the right place. if you're able to get the complete bulkhead dash harness, do it (along with the 5MT ECU). otherwise, read on...
since i haven't been able to find anything clear online to be completely successful, i ordered me the FSM and picked my brain with a ton of wiring diagrams. i'll only be explaining my process as done on my 05MY FXT. though, the premise of this process should apply to other models as well.
for the wiring underneath the car and to keep things plug-n-play as much as possible, i reused the existing 4EAT harness and repinned as much as i could.

left: 4EAT sensor harness with the three sensors (torque converter turbine speed, front vehicle speed sensor 1, rear vehicle speed sensor 2)
right: 4EAT harness for inhibitor switch
i'm on a 5MT ECU, now. but even when i was running the 4EAT ECU, i still was not using the 4EAT TCM and was able to get around town. no matter what combination of those three plugs i had plugged into the TCM, my OBD-ii port wasn't functional. i couldn't use either my AP or a code reader tool unless i removed the TCM. so, i left it out. because of this, instead of running separate wires from the tranny into the cabin, i reused what wiring was already there that ran between the tranny and the TCM.
the following items are what will need to be tackled:
- key interlock switch
- clutch switch
- reverse light switch
- neutral safety switch (nss)
- vehicle speed sensor (vss)
here's how to read the pin numbers for the Male and Female plugs...
key interlock switch
so you can remove your key from the ignition, you'll need to jump (forgot what pin numbers) the black and the white wire. i reused the wiring from the 4EAT shift lever assembly that included the lightbulb...
clutch switch
i used this so i can start the engine like on any other MT vehicle. from the clutch switch, i ran a couple wires down to pins 11 and 12 of the 4EAT inhibitor switch harness. this is to mimic Park/Neutral. (this is the only separate wiring i ran. i'm sure i could have used existing wiring like i did with my vss process, but that idea came later. and there were enough wires left to do so.)
reverse light switch
reverse switch and nss are joined to a 4-pin connector. i repinned 2 and 4 to pins 9 and 10 of the 4EAT inhibitor switch harness coupler.
neutral safety switch (nss)
reverse switch and nss are joined to a 4-pin connector. i repinned 1 and 3 to pins 1 and 4 of the 4EAT inhibitor switch harness coupler.
vehicle speed switch (vss)
(NOTE: it's important to understand that i'm using the wiring that ran between the tranny and TCM as a way to avoid running my own separate wiring. because of this method, i highly encourage not plugging in the TCM!)
the 5MT vss has three wires (signal, ground, power)...
speed sensor 1 of the 4EAT sensor wiring harness has two wires. i used one to run signal up to the cabin; the other to run ground up to the cabin. the
speed sensor 2 of the 4EAT sensor wiring harness has three wires. i used one to run power up to the cabin. that covers all three wires of the vss up to the cabin.
vss pins (sensor on tranny):
pin 1 // signal
pin 2 // ground
pin 3 // power
4EAT sensor wiring pins (reused harness from inhibitor switch):
pin 14 // speed sensor 1 signal used for vss signal
pin 18 // speed sensor 1 ground [this wire is shielded to ground as well] used for vss ground
pin 9 // speed sensor 2 blahblahblah used for vss power
those three lines run up to the middle plug (medium-sized) that plugs to the TCM. (REMINDER: you're not to plug the TCM!)

^
tap from B55 plug (middle plug)
pin 6 // signal line
pin 15 // ground line (just ground this to chassis)
pin 24 // power line

^
to B56 plug (larger plug)
pin 1 // signal line (runs directly to both speedometer and ECU)
pin 31 or 21 // +12v IG ON line
(should you decided to keep the TCM, starting from the vss, you'll have to use another ground and power source. for the signal, you may still use pin 14 of the sensor wiring harness. for the MT, the speed signal goes directly to both the speedometer and ECU. for the AT, the speed signal goes to the TCU first, then to both speedometer and ECU.)
(this post will be updated as needed to better clarify exact plug identification pin/wiring colour, etc. as i go back and review diagrams, notes and pictures.)