The interior and transmission will definitely interchange. The engine is at least mostly the same ... but there may be some minor differences in sensors or something. I know more about the non-SC Thunderbirds, so hopefully someone else will chime in about that.
Basically they are the same main differences are the supercharger itself which Ford made more efficient in the later mods and the radiator in later mods was crappy plastic as far as the engine area. As far as the interior stuff from 89 to 93 most of it will trade out..
What to do. If you are going to change out the engine use your inlet plenum,
Throttle body and maf. You dont want to use the throttle body with the coolant lines that run through it.