What are you doing? Putting in new axles? new bearings? new seals?
I got new one piece Genuine Gear axles for my AMC20 and it had instructions for the shimming and the tolerances. I don't have the instructions with me because a friend of mine is using them to install the axles at his work.
If you are just installing new bearings, or new seals, you shouldn't have to worry. Just press it all together and you should be done. If you have something rubbing, you probably didn't seat the bearing all the way down, or you pressed it on too far. I remember reading in my axle instructions not to press the bearing past the raised part of axle. That is where the seals goes.
2004 Rubicon, 6" lift, 35s, winch, hard top, full doors, bumpers, tire carrier and rock sliders.