I am not exactly sure of what your saying the problem is. Is the screw wobbleing out of round?
There are a few things that could cause this, but first is it normal? Even a lower cost screw & nut setup would normally run pretty true. I wouldnt expect perfection but .060 thou is a bit much.
But first you need to figure out what & why is out of specs. I would remove the screw & take the nut off. If you have not ever done so then you need to research & learn how to do this without causing damage.
Then take the screw & check to see if its bent, plus measure the depth of the threads to see if they are right ( different places & all around to know if they where cut on center). Then the machined ends need to be check to see if they where cut on center. Even if the screw is OK if the machining of the ends was done off center then it could cause movement of the screw when its mounted & rotating.
Its doutefull the ballnut itself would be causing such a problem with it being mounted stationary. But yuo should be able to feel such a thing when you remove the assembly by rotating the nut. I would expect the ballnut nut to move smoothly unless it has some kinda odd problem.
There is a good chance you may need to replace the screw, but first you need to know whats wrong. It is possibly to straighten a bent screw if you do it right. BUt if the ends where machined with the screw bent then its probably not going to help. One good thing is the screw stock is fairly cheap compaired to the maching & ballnuts so maybe its a cheap fix if you can pinpoint the problem.