Thanks for all the replies. I am concluding that I should square it up as best I can before machine is under power. Then when it is powered, cut some test pieces, measure, and adjust from there.

My thinking for the Z axis is to mount a piece of drill rod in the router collet, mount a dial indicator and check for runout in the x and y direction as the Z axis is run up and down. I am guessing that should be done in a few different spots on the machine.

I have to laugh when I think how I square my table saw blade. I did use a dial indicator to set the rip fence ( Beis clone), but only one end of the fence is clamped down, so it must move some. Then I usually square the blade to the table by eye with a square. This seems to work okay for the simple cabinets/boxes I build. Luckily, I have avoided building space shuttles in my shop, so far.

This stuff can drive you crazy if you think about it enough.