Thanks to PaulRowntrees program warp drive I have resolved most of my inaccuracies. With Pauls warp drive program I was able to find that my machine is about .15 degrees out of being orthogonal.
I have a new problem now that I have not been able to get figured out. I am making custom computer cases and the fan grills that I make are half circular arcs. On one side the archs are perfect every time and on the other side they vary pretty substantially. Attached is a picture of what I am talking about. Left side good, right side bad :tired: