After a good cleaning of the area, install your pilot bearing. If you use roller bearings, make sure to put the seal out. It's the end that looks like it has a "cap" over the bearings. I use a socket that fits the OD of the bearing and tap it in. It needs to be flush with the end of the crank.

http://img.photobucket.com/albums/v228/Avette4me/Vette/Tremec/install/01.jpg

The flywheel goes on next. I used a pair of vise grips to hold it stationary when I torqued it (60 ft/lbs).

http://img.photobucket.com/albums/v228/Avette4me/Vette/Tremec/install/02.jpg

The clutch kit purchased, had a traditional non roller bearing pilot bearing. Does it matter if the flywheel goes on before the pilot bearing. The pilot bearing sites in the crank shaft in a seat, so long as it is the seat does it really matter which goes first? The flywheel was in place first, so if it does matter this could be the problem.