During assembly, the main shaft rear race and bearing must settle into place. The tail housing has the "seat" where the race is held in place. If it was not properly seated, it would have seemed tight after initial assembly. If you don't have a dial indicator, I'd just add shims to the input shaft retainer until it has no perceptible play by hand but still easily rotates by hand. It sounds like you are on the right track by eliminating countershaft play as well. Is this a non world class T5?
