@joekorman When you say that on a 6" square piece, you are out by 1/16", do you mean that you run a job on the Mill that is a 6" square and, measuring the diagonals, you are out by 1/16"?
What is the “sandwich block”, and how are you using it? From your description, I’m thinking that it is a piece of wood that fits precisely between the two back feet when they are tightened. Then you move it to the two front feet, squeeze them until the block precisely fits between the front feet, then tighten the front feet. I am thinking, though, that I am missing something, since doing only this would guarantee that the Y rails are parallel to each other, but it would not mean that they were square to the X gantry.