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Could it be the 97-00 and 01-04 use different size MAF'S?
Someone hopefully can confirm, but I am sure I read somewhere that the early cars had slightly different injectors. They actually have smaller throttle bodies, though.
I do know that some of the vacuum tubing is different, as when I got my Halltech Stinger labelled for 97-00 (mine is an early build '98), while it was the right diameter, I had to drill a hole in the air bridge for a sensor that was outboard of the throttle body. Not there on all years it seems.
I think GM was trying to get emissions lower on the later cars - don't they have extra cats? Cats = restriction.