If it won't even bolt up without the clutch then something is off further than I've ever seen before. So the tranny bolts up to the bell when it's not attached to the engine right? And the crank is drilled deep enough to accept the input pilot.
Gus

64 Plymouth Savoy
493 Indy EZ's by Nick at Compu-Flow
5-Speed Richmond faceplate Liberty box
Dana 60