You have an incorrect pilot bushing. There's a bushing with an oversized OD that was intended to be used on crankshafts that were originally mated up to a Powerglide automatic. If you pound one of those bushings into a crankshaft with the proper diameter counterbore, it shrinks the center hole so the trans input shaft has to be forced into position. Then the clutch won't release. I've encountered that several times while sorting out a botched do it yourself clutch installation. Yank the pilot bushing and install the right one. The transmission should be an easy slip fit.
Jerry

"It is better to be silent and be thought a fool than to speak and eliminate all doubt!" - Abraham Lincoln
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