I use a pair of 1/2"-13 x 2-1/2" bolts with the heads cut off, rounded, and screwdriver slots cut in them to install in the top two trans bolt holes in the bellhousing; that guides the trans and input shaft squarely into position and takes the load off the clutch disc during the install. If you still have a problem, have someone step on the clutch once you have the trans almost all the way home and it'll pop right in. Then remove the studs and replace them with the trans bolts.
I also use a plastic plug on the output shaft to keep the lube in the trans while you're wrestling with it.