I asked the guys at the MSS this question years ago - the answer is that if it is the same model (N/A vs SRT) you are fine, just DO NOT change the ECU, leave all electronics alone.
Just swap the engine.

IIRC, with the automatic, you can transplant the TCU or not - that is your option. But I admit I can't remember for sure, seems like they said to NOT to changing TCUs.

@GannyX , what do you say, James?