Dave,
What I had to do was move one of the stepper motors (gear box) on (our) Y axis. I losened up the 4 screws and drove the set screw to push the gantry the direction I needed. I hope I have it corect now if not I will have to start from scratch cause I'm to the limit now as far as movement goes. I checked as close as I could and seams correct now. The things we learn the deeper we get into this. I did then adjust the one limit switch but they are a pain in the A#$ to fine tune. When you look at the picture of my new jig the right side was off by more than 1/8". Did the adjustment, made a new X and Y rail and re routed it square.......
Will