As I understand it, the ecu is compatible with the wiring harness specific to that ecu. When swapping trans you don't touch the wiring harness or ecu, and the ecu could care less what transmission is in the car as long as it has the correct wiring harness to go with the ecu. So, if you swapped out the ecu, and didn't swap out the wiring harness that goes with that ecu (I think it's the 02 sensor portion of the harness that might be specific to the ecu) then you would ave a problem.