This is probably an old trick that most everyone knows, but it helped me alot to use a couple of transmission bolt guides. These are extra long bolts with the heads ground off and I put them in the block where the transmission bolts would go before trying to join the engine and transmission. They help guide the two together. After the engine and trans are together correctly, put regular bolts in the available holes, take out the "guides", and put bolts in those holes.

Andy

Real fun takes hard work.
'83 Short bed, NV4500, 33" BFG MT