If i remember there were a few bolts on the bellhousing and diff size ones they are not all the same. If you are not pulling the trans then jam a screwdriver between the block and bellhousing also i think there are a few small ones on the bottom of the bellhousing for the inspection cover.
I ran into something similar when I was pullin my engine, there is a small screw on the bottom of the bellhousing that holds the spacer inbetween it & the engine, if you don't remove it, the two won't come apart....
Did you pull the clutch off? if so did you use the alignment tool to re bolt it? Also what i do is put the truck in gear once you have the shaft into it and when its real close then rock the truck in gear and it will turn the inputshaft to help line it up. Make sure the motor is the same angle as the trans.