!. If the pilot bushing is dinged on the edge even a little, the input shaft won't slide in, so check that. (Don't ask me how I know)
2. Many people find it helpful to get some long bolts the same thread count as the tranny bolts. Cut off the heads and thread them in to the bell housing. They make lining up the trans a lot easier. Then when you get the trans seated, replace the bolts with the real ones.