a 3800 is a 3800, end of story, it will fit. 97-08 engine will fit in any year grand prix. you may have to change the exhaust manifolds or the intake or TB, but whats that? nothing really. you already have the parts on your engine, just swap over whats needed.
if you go from n/a to super charged the mechanic cant fix that issue, you need the pcm tuned to run the s/c engine to its fullest potential.
so either get a canned tune from one of the vendors, or find a local to help you out with a tune.