While I assume that you may have already uncovered this trick, I'll share anyway.
If you are installing a transmission that has a seperate bellhousing (such as the Borg-Warner T-5); install the bellhousing onto the engine block first. Then use a 2X4 to fully depress the clutch peddal. Now the clutch disk is fuly floating and free to rotate and move as you install the transmission into the vehicle. This allows more freedom of movement as you install a transmission into a tight chassis (much more than trying to align the input shaft with a fixed clutch disk). Once in place install fasteners as normal.
I've had good luck with this technique and i hope it helps.
If you are installing a transmission that has a seperate bellhousing (such as the Borg-Warner T-5); install the bellhousing onto the engine block first. Then use a 2X4 to fully depress the clutch peddal. Now the clutch disk is fuly floating and free to rotate and move as you install the transmission into the vehicle. This allows more freedom of movement as you install a transmission into a tight chassis (much more than trying to align the input shaft with a fixed clutch disk). Once in place install fasteners as normal.
I've had good luck with this technique and i hope it helps.