I agree with most of what stsalvage says, but to line the engine and tranny back up all you need is a couple of long 3/8's bolts (I used starter bolts cuz I had them, but they're not cheap). Cut the heads off of the bolts and use a grinder to square the ends some (just enough to be able to turn with a pair of pliers). Put them in the bottom bellhousing bolt holes and use them to line the tranny and engine up. Then you can start the bolts in the next hole up. Granted I've never done this putting the engine in with the tranny in place, but I've used it several times to stab the tranny with the engine in place.
