In short, most of the powertrain and electronics that go with it. 3.8 V6 transmission won't bolt up to a Modular V8 (would bolt up to a small block), so at a minimum the transmission, but if you've got a 7.5" rear end, it probably won't last long behind a V8. Electronics should require a fair bit of rewiring, at least a 97 4.6 in a 98 did.
Personally, I wouldn't do all that for a GT 4.6; the amount of work to get a 4V in is about the same, for far greater potential.
Exactly what he said, I picked up a 02 gt 5speed 100k miles for only 3k, your gonna need the engine, ecu, exhaust, and worst of all, labor. More work then worth if you ask me