It is a bit hard to duplicate what is going on here, so let me try to illustrate and explain. The hub is the only part that is touching the tabletop, so any imperfections in the tabletop does not affect the measurement above, which is the difference between the cup and the bearing and hub, measured by a straight edge, in this case. In this picture, I took the existing .002 circular shim and put it in the area that the shim is to occupy, and it raised the straight edge leaving a space between the bearing, cup and the strait edge, when it should be level, if it is the correct shim. The measurement needed is between the cup and the shimming tool, which I do not have and is not available, so I am showing it with the straight edge. The manual shows a picture of the shimming tool in a similar set-up to the caliper, if you reference my previous picture, and you will also see that the straight edge is level across the three items, which indicates that it shouldn't have any shim, as you use the shim to make it level. The manual also says that you need a minimum of one shim, and not more than two. So, my choice seems to be between using no shim and having the three level; or putting the smallest one available, which is a .002, which I have in my possession, as it says that you should have a minimum of one shim.
So, neither option seems correct, but I have to do one or the other.
Or the levelness may indicate the bearing or the cup is worn down a bit, as the bearing and cup are angled; and I should get new ones, although they appear to be okay. This is probably the only logical explanation, and it's only $30, so I guess that us what I will do, and maybe order an extra .002 shim, in case it comes out with a bigger space. Seem right?