The Mechmates are a really good looking design and I would have gone that way if I hadn't got most of my build out of decommissioned gear at work which dictated the design by the components I had.
Being dual slave drive rack and pinion (thats right?) dialing out any skew should be a breeze. What I would suggest you do is put two thin DF of other scrap sheets down an cut thru both a big square. Then flip the boards face to face along the X axis this will double your skew error that you can measure between the two pieces and use this value to rack the gantry. Loosen the gantry to drive sides and adjust your home sensors accordingly.
Now rotate the top test piece 90 degrees and compare the X and Y dimension and adjust you tuning as needed.
But first...check that everything on the machine and drive are snug with minimal backlash etc.
Probably telling you how to suck eggs.. I 'm sure if you built the machine you can tweak it to get it right and probably to within a fraction of a mm accurate. Just don't loose sight of what it is your cutting and the processes afterwards to the part .. lots of small variances disappear in the end product but getting stuff square is importatnt because of the doubling effect when you flip parts (think forms and mirrored sides of the floats)
PM me if you need any help.