OK. Then your problem is not mixed version parts. The Rev A part is 1/8" longer that the base or original parts. Your problem is an out of tolerance part. As it is unlikely that wear from use is the culprit, my guess is that it came from the vactory that way. You have two choices - replace it (Clausing may still carry the part). or shim it. Check on some place like McMaster for bearing shims, inner race shims, outer race shims. You might also try a place like Ace Hardware. You would pay more for one shim, but you won't have to buy a box of them to get one. The shim OD must NOT be any larger than the shoulder diameter. It can be a few thou smaller.
Another possibility, if you have the necessary tooling, would be to reduce the thickness of the hex head.