I have seen somewhere that builders have used a laser to insure that the X axis gantry is built to be square with the Y axis rails.
My Y axis (48" extrusion) rides on 1" linear rails, there are two trucks 7" apart (on each end) bolted to a rectangle of 1/2" 6061 Alum (truck plate). The X axis 72" extrusion is bolted to the truck plate by six pieces of 1/2" 6061 alum.
I'm positive either one end or the other truck assembly's is not square to the X axis (gantry).

I need to tear it down and refine the alignment to the X and Y axis, a laser comes to mind but have no idea as to how to do that, but am open to other methods as long as the results are a more precision machine.

Here are a couple of photos of my machine construction.