won't go in gear

.0055 should not hurt you The issues:

1---some cranks were never drilled deep enough if they were automatics. With the trans out, measure to the bottom of the crank hole and compare with shaft length to the face of the gearbox

2--Runout-- and bell square. Did you check both? You need to check that the bell is at 90 to the centerline of the crank. You need to check runout of the crank to the bell hole Two separate checks

3--Tight pilot. I would think this is rare, but again if you had an auto crank, and just a little undersize (many are so far under that the pilot won't go in) but if it's just a LITTLE under it would squeese the pilot and make it tight.

The sure fire check would be to remove clutch/ pressure plate and install just the gearbox and see if the trouble is still there.

Another approach you could take AFTER checking pilot hole depth is to abandon the old pilot (remove it) and use the later model Jeep style pilot which fits into the torque converter recess. You can get them in both bushing and roller. I would not use a roller on a worn pilot shaft.

Like so