The 4.6 is wider than a Boss 429 so it won't fit with shock towers. Also as cool as they are they are small (281 cu in). I'd much rather swap a 5.0 HO in and it's almost bolt-in. With stock suspension their will be some issues. The late model 5.0 has a double hump oil pan that won't fit but switching to a 289/302 pan is easy. The 5.0 has the dipstick in the oil pan but the timing cover can be drilled to put it in the same location as the 289/302. The 5.0 also has a serpentine belt system which spins the water pump opposite of the original 289/302 and is designed for a cross flow radiator so the inlet/outlet are on opposite sides. Not a big deal but will have to be dealt with. Their are aftermarket wiring and computers to plug the late model EFI into a classic without much pain. You couls use a T5 or AOD also and get overdrive.
here is a very helpful link (Jame'sW)
EFI 5.0 install