Having done this recently and having the same problem, here are a few things that might help.
A clutch alignment tool will help you since you can match the splines directions on the clutch and the transmission shaft to make it as close as possible, that way any misalignment will work it self out.
One of the few times I would disagree with Jerry.
Once you get the shaft into the clutch and the transmission as close as you can, use the bell housing bolts to slowly draw the transmission and the engine together, I think I was able to get three of threaded, on one each side and one near the top. Do this carefully and slowly, a few turns each time, alternating bolts, moving the transmission evenly until you get it mated up. You want it to be slow, so you don't crack the bell housing. That was what worked for me after probably an hour trying to muscle it back together, a mechanic friend suggested I do it that way.