If the pilot tip of the transmission is binding in the pilot bushing of the new engine, then the input shaft remains energized by the engine crank even though the clutch disc is disengaged (if the engine is running). That situation makes shifting very difficult if not impossible when the engine is running. However, when the engine is off everything will shift normally. Just a possibility.

Last edited by Lugnutz; 10/31/2020 1:37 AM.