I believe that my Z axis isn't perfectly perpendicular to my table. When I flycut my spoil board I get small (.001") ridges, which indicates that the spindle is skewed in Y a bit. And when doing a pocketing cut my clear cut (.25 end mill) and my detail cut (.060 engrave bit) are at slightly different depths, which could be due to tool diameter if Z isnt perfect.
What is the best indicator/method to align the spindle?