Even changing RPM's will give a different amount of run out.
It's pretty much not going to be exact (.001"), anytime you change something, until after your test run, so you can calibrate for the different materials, feeds, speeds, etc.
At least give yourself a little tolerance if possible.
My son spends hours getting everything within .0005".
Next day leans on the machine, and has to do it again.
Drives me nuts