When I rebuild a NV4500 I do not use a dial indicator to set bearing play. I get shims in quite a few sizes. When installing all new bearing I make sure the bearings are properly seated on the shaft and that there are no burrs or debris in the housing that prevent the races from seating properly.
I then install and shim the counter shaft so that I can just so turn it by hand, it's pretty tight! Then I install the main shaft and input shaft and shim the main shaft the same way which can be tricky if it's your first time. You've got to be sure that you're feeling drag only on the main shaft when you try to rotate it.
Once the trans has a few hundred miles on it the bearings tend to loosen up and at that point instead of being too loose, everything is within spec. Just use common sense when setting them up this way because you can only put so much pressure on the bearings before you start to compromise the integrity of other parts. Also I've been installing 5qts of 75W-90 full synthetic gear oil which seems to greatly extend trans life!
At this point I'm fighting 5th gear syncro cone issues, the splines break out too easy and I'm not exactly sure how to fix that. Maybe key the cone to the counter shaft?