When it comes time to just the long block (engine by itself) all the D23's are the same from 03-07. The 03-04 PZEV models will have an aluminum valve cover however.
As far as a tune is concerned, Turbo Tom will be your best bet. For $400 he'll ship you out an xcal 3 with a base tune to start with. Then he'll have you data log the car and email the results back to him so he can send you a final tune with any precise adjustments that need to be made. He also gives free update tunes for life unless you go F/I later.
He's pretty big on the forums so just look for him and PM him with any questinos.