i would suggest a mail order tune just to disable the VATS system so you con proceed with the swap and work all the bugs out. Once the car is up and running and driving, then take it somewhere for the performance part of the tune and to make and other changes.
I put a 96 LT1 in a '79 y-body and used a stand alone harness which came with a module that bypassed the VATS separately and my ECM is still 100% stock. Ive ran the car a few times but due it was a long term project and now just sits. If it had ever been finished, then i would have taken it to get tuned.
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