I found why the transmission wouldn't mate up with the engine and I'm definitely smacking my forehead over it...
There is an alignment dowel near the top of the bellhousing, next to the top passenger side bellhousing bolt. This dowel was present in both the block and the bellhousing. Duh.
It should go together just fine now but I have to wait for the weekend to find enough time and a pair of hands to help.
