I am having trouble following as it seems that you have different problems at differnt time in this thread.
The latest seems to be a problem seen prior where the transmission will not fully engage the clutch and pilot bearing preventing the transmission from meeting up with the bell housing. I thought that one had been resolved with clutch disk alignment?
Previously you had it all together and it appeared the clutch was working but the transmission would not shift into all gears.
Prior to the latest clutch I believe you were installing the original clutch after it had been refurbished which should have resulted in the same stack up as the original drivable version except with a resurfaced flywheel and restored clutch disk lining that had clutch slippage and started this whole process.
Maybe you can recap what problems you have had, how they were resolved, and what the latest problem is so that we can help determine a path to success.
