We had a great discussion about this recently. The short version is - geometry.
Gently insert a 3/4" copper pipe abut 2 ft long through the clutch into the flywheel . Measure &/or adjust the angle of the tube relative to horizontal. Figure out a way to align the input shaft perfectly to the plane of the tube. Remove tube .Mate up. It is very easy to get the gearbox input shaft a few degrees misaligned left/right, up/down - because there is no leveling bubble on the engine and gearbox to guide you.
You need to fiddle with levels and bubbles to do this. I think it is worth the effort because just brutally tightening the bellhousing bolts could cause issues.
I am sure you have tried rotating the input shaft a few degrees back and forth while trying to coax the two parts together so logically it is an 'out of level' problem.
I think this is why some people remove the cross member and mate the engine and gearbox while they are both out of the car. Even then it is difficult.
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