Okay, first of all, let's clarify something. Manual transmissions require a flywheel, and automatic transmissions require a flexplate. The two are not interchangable. That being said, if you are using the flexplate from the truck engine, then the truck engine had to have been paired with an automatic transmission. Thus, there is no pilot bearing to worry about. You probably don't have the torque convertor seated all the way. Try slowly rotating the crank center bolt from the front while someone else is trying to bring the engine and tranny together. If this fails, raise the back of the vehicle off the ground, put it in gear and have someone turn the back wheels while trying to bolt the engine and tranny together. This should allow the TC to align correctly.
Take care,
-Chris
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