Is the pressure plate bolted down tight? If so, try loosening it so that it just barely keeps the clutch disc in place. This way, you can move it around a bit when you try to put the tranny in. This can be done because you have a removeable lower inspection cover, and can tighten the pressure plate bolts up afterwards. Another way would be to hook up the clutch fork, and have someone push in the clutch when you try to install the tranny.
Were there any locating pins between the bellhousing and engine block? if not, the bellhousing may not be centered properly. You might want to get a dial indicator and a magnetic base and check for runout on the tranny pilot hole. The procedure should be in the shop manual. Even if the pins are there, that doesn't mean it is all lined up perfectly.
