It looks like my Y-rails are slightly off parallel, and not square with the base/wasteboard of the machine. It also looks like the X-rail is not square with the base of the machine. I’ve used calipers to determine that all of the feet are exactly the same height off the table (though I don’t know how much of an impact this makes).

I’ve seen mentions of using clamps and brute force to square this all up, but I don’t understand the particulars of this (to what do I attach the clamps? How do I apply brute force? How can I ensure squareness/parallel while applying brute force?). Any recommendations for sources - preferably video, but an article with pictures would be great - on how to actually go about squaring up the machine?

Squareness has to start somewhere – good job determining the base is level.

Now start at a corner and determine in what way it is not square, machine or shim until square, then repeat at the other corner on that axis, then square the X-axis on that side, then square the two corners on the other side, then the other side of the X-axis.

If the machine is not square it should be a lozenge shape — brute force it by putting clamps across the longer diagonal, loosening the screws, tighten the clamp until square. then tighten the screws.

Thank you for your advice and suggestions. I got the machine quite square, and it turned out I was having belt stretch issues. I’m finally calibrated and all set!