I'll assume you are doing a 3" BL since that is the standard kit size.

The shifters need to be extended because the body is now 3" further away from the transmission/t-case. You may have to do some bending the shifters as well, or cutting to the tranny tunnel, or both.

Its "better" to lower the radiator down and keep the full shroud than cut out the shroud. I know several people have gotten by with mutilating the shroud; but its really not much work to just drop the radiator.

The exhaust is hung from the frame, not the body... or at least it should be.