[Gearhead999]

Pilot bearing most certainly could cause it. Also, do you have the dowel pins in the back of the engine that align the bellhousing?? If they are missing that too can cause it.

When you installed the clutch did you make sure everything was clean and grease free??

Lastly, when installing transmission you didn't force anything, like using the transmission bolts to "pull" the transmission in. You didn't hang the transmission on the clutch without having it bolted in.