I have a 2002 mustang V6 and a 1998 mustang gt 4.6L V8. I want to swap everything from the wiring harness to the rear end will everything bolt up just fine or will I have to modify a lot of stuff
Can be done, I would personally stay away from it because the 98' has the NPI engine. If the 02 and the 98 have PATS then you will have to get that sorted. I can't remember if the 98' MY GT's came with returnless fuel system or return, I'm sure someone else could answer that. I think 98 made some changes to the fuel system. You will need to figure out COPS vrs the 2 coil packs the 96-98 GT's used stock.
In short the best way to do it IF you really wanted to would be to use the 98' engine and find all the supporting hardware for the 99-04 GT. engine harness, COPS, PCM, ETC. Your going to need a PI front timing cover and a PI intake manifold for COP bolts.