So you have a Light Duty 3-sp, if the trans has half of the bellhousing cast as part of the trans case.
Have you tried adjusting the clutch linkage? At the clevis inside the frame rail?
Did you remove the cross-shaft and fork as part of the rebuild? Any chance the fork is in backwards?
1952 F-1 Flat V8 3-on-the-tree
MSD, Rochester 2G, Red's Headers