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?
I guess that it has been too long since I do not remember doing anything unusual when I changed Willard from the original light duty 3 speed to the HD 3 speed. My memory was that it was a stock bolt in using the same clutch and driveshaft. Willard was running a 56 Buick Nailhead back then (the reason for the change to the HD 3 speed).
I think that I did it in 1978 so memory is probably a problem!