I ran into something like this before.
Mine was the wrong pressure plate.
Okay, there are basic things you can check.
1. Ford or aftermarket crank shaft. Silly as this sounds, I had a crank that had an added .050" on the end that was supposed to be cut to make it true.
2. Ford or after market flywheel. If the flywheel is setting out further from the block, this will cause the problem.
3. Is the flywheel bolted up against the crank? If you have it kinked, it will never allow the bell housing and trans to bolt up.
4. The pressure plate does cause this problem.
5. Is the stub all the way against the pilot bearing area ( hitting the crank ).
This is more common than you think on older Fords as the China made clutches are not always cut right. Lay the clutch against the flywheel and see if it is flat on the surface.
6. New Ford or after market input shaft? The shaft itself could be too short. measure it. It like 1 3/8". Someone like David Kee could tell you.
7. Bearing retainer too long? The collective depth should be less than the hub distance to the face of the bellhousing.
May I recommend this test? First, I removed and installed my trans and clutch assembly several times and this works for me ( do what you want ).
With the block on the chain, install inspection cover, flywheel and lock all bolts. Check the flywheel is seated all the way.
Install clutch disc with big nub in and pressure plate. leave bolts loose.
Lift trans to engine and see if it makes it without the bellhousing.
If all is good, place the bellhousing in place and see what happens.
All these other people on this site are telling you about the same thing.
Let us knw what you got.
Just my $0.03
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