I had a quick look back through the thread after I wrote my last post (thread started a long time ago!) and it seems that you are driving both gantry ballscrews by belt from a single stepper. In this case you could adjust gantry squaring by tweaking the belt position on one or other of the ballscrew pulleys a tooth or two at a time - I guess that that is what you were planning? I was able to just move a home switch trigger point slightly but at the cost of doubling up on steppers, drivers, switches and wiring, and general configuration complication!