How about setting it up as accurately as possible by measurement, then cut two right-angles in a piece of panel material - one cut across the bed to give a straight edge, then one cut along X at mid point of gantry to divide it in two. Flip over one piece on to the other and the difference between the two "right angles" is twice the gantry alignment error. I was thinking this one through the other day as part of my "how would I set it up accurately?" musings but not sure how it would work. I was also wondering how and where I would build in the necessary adjustment for correction.