Rick,
I put a later model bellhousing, 1962 truck, behind a 54 car 235. Also changed out the flywheel and starter. I must have gotten lucky because it bolted up fine with no driveability problems. Definitely replace the pilot bushing. I didn't and got to do it over. A $2.00 part that cost me mucho grief. New throwout bearing also great advice.
I ended up modifying a clutch pilot tool so it would fit properly. You will know the clutch is out of alignement when you spend 30 minutes trying to get the transmission to bolt up and it won't.
A simple way of removing the pilot bushing is filling the bushing with play dough and then hammering a wooden dowel (sized to fit in the pilot bushing hole) which creates enough hydraulic pressure to force the bushing out of the crankshaft end. Wear some goggles as the play dough may spurt out a bit, but it works better than grease.
