The splines of the input shaft might be hitting the bushing since it is now closer to the trans an the one installed in the hollow of the crank. Another thing to try is once you ve it that far try to depress the clutch , either linkage connected and have someone push in the pedal or a pry bar on the fork , if the disc is a little off it might be binding.

The other is if the engine and trans are not factory original to each other you might have too much runout which is being made worse because you have a tighter fitting bearing closer to the bellhousing. I just discovered that the engine and bellhousing are machined as a unit originally so swapping parts can cause a runout issue.