so I know you guys have probably heard this question hundreds of times but I bought a 3.4 the other day for $550 it's going into my 91 with a 5 speed and it came from a automatic 97 4runner and i didnt come with a wiring harness I need to know if I can use a automatic wiring harness with a manual ecu and make it work out.
This is exactly what I did. I have a 92 pickup, 97 Runner 3.4 and used the stock auto harness but repined it to a 97 manual. I bought a 97 Manual ECM and everything works fine and passed the strict California laws on motor swaps. Get the same year and model ECM just manual as there are differences between the Runner and taco motors such as EGR etc.
I have a fairly decent swap thread and detail the process from beginning to end...........well almost end cause I dont think that it ever ends......Not the swap but everything else.............I address exactly what you asked about
http://www.yotatech.com/f160/had-officially-began-3-0-auto-3-4-manual-92-ex-cab-196823/index11.html