96 Sunfire w/00 2.2 Cavy engine

Ok, I have a 96 Sunfire that originally had a 2.2l engine & tranny in it. I bought and had put in a 2000 2.2l Cavy engine and tranny into my sunfire. My car would start, the rpms were high, and then it would cut off. I took it to a shop and the guy tried to reprogram my computer.. he said it wasn't holding memory. The computer under the hood on the passenger side is 00 and the epu under the driver's side dash is a 96. He said the 96 and 00 computers don't "jive" so he wants to swap my 96 dash and elecs for a 00, to convert all my electrical stuff from the dash to the engine a 00. does that sound right? what should that approximately cost me? thanks