I am trying to fine tune my  router and am having problems with squares and circles. I have run through the sequence of step per inch mode. I tell the program to move 20 inches and then tell it how far it accualy moved. In all three axises I am in tolorence of .0001. When I try to machine a circle and square I am geting ovals and rectangles. In a program that created a g code to run a 9 inch square I am getting a 9 inch run in the y axis but only around 4 inches in the x axis. the same thing is happening when I run a circle. can anyone tell me what I am doing wrong.

Either your steps per are not right, your code is not right, you are losing steps on an axis or you have axis scaling on one axis.
How close mechanically are your X and Y in configuration, ie is it the same screws and motors and drives? How close are the steps per unit in the two? Hood

Also check that your stepper motor shafts are tightly coupled to your lead screw. The motor may be turning, and your shaft isn't.
That will render weird circles and other shapes as well. I had this issue where a screw vibrated out of my coupling.