Fox Computer Swap with Transmission

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How does it run?
there is something about the o2 wires, something about a jumper, what year are we talking about and what computer is in it now?
it's a 91 LX 5.0. It has a new engine with 500 miles and doesn't run that good until it gets warm. This is similar to how it ran before the new engine. I don't know what computer it has yet, I haven't looked. I'm just curious since I found out it was an auto to begin with
 
Not necessary. I swapped mine 10 years ago and still retain the AOD complete. Changing over to the manual ECU requires swapping a hardness and repinning the o2 sensor harness jumper, but it should run fine with AOD ECU.

I'd pull the codes to start and see if anything comes up as a first step
 
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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.