lippy,
My experience is with a small block into an FIA, but I would think the process would be very similar. Like ERA recommends, I would install the motor and transmission separately.
Good idea to have Brent install all the clutch components … TO bearing, fork, bell housing and starter … making sure things lined up. As Dan suggested, cut the heads off (2) extra transmission bolts and put into the upper holes of the bell housing to use as guide pins. Do a test fit of the transmission out of the car. Take the guide pins out and remove the water pump pulley & alternator and install the motor without the transmission. Once it's in place, with the seats out and no trans tunnel, the transmission should slide right it and bolt up no problem. As I recall, there is a boss on the TKO 600 that needs to be cut off, it's in the manual.
Along with covering the fenders, tape some cardboard on the aluminum fire wall to keep it from getting dinged up. It helps to have about three or four guys to help guide it in, and help you to celebrate when it's in
Are you going with an internal TO bearing / slave cylinder or external slave cylinder? I would recommend the external, easier to fix if it leaks … but see what Brent recommends for your setup.
Don't forget to take some pictures of this milestone, you are making great progress!