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If the engine is the same model, you shouldn't have a problem. If there were that much of a variation, I would think you would have more of an engine issue than a trans.
Besides, the TCM only communicates with the ECM, so if they replaced the ECM with a wrong one, then yes the TCM may not work properly, otherwise probably not.
If they have to check the wiring, I would question whether or not they even did the engine replacement
properly or if they damaged anything during replacement. Don't forget to ask, ask, ask "Why oh why oh why are you doing this or that???". It's your right to know. You should not have to pay for someone else's mistakes.
Also, it sound like a different shop did the engine replacement. Make sure you get proper documentation
as to the cause of the problem in case the other shop did mess up.
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