FWD will be a pain in the ass. The "easy" MTX-75 can't handle the torque of the 4.6.
Other FWD manual options are the MTX-4 from a 1989-1995 SHO or the transmission from a first generation Mazda 6 V6. The 6 uses a adapter plate from the factory to fit - so it's possible that you could use this to your advantage to either modify the plate or build a new plate to your specifications using the factory plate as a template.
RWD, the world is likely your oyster. If you tear down the block enough you can probably start putting mustang parts on it.
