When I put together my MPCNC I did the following steps to ensure I had a square working area.
Used a square and some geometry (345 method) to layout my work area as a true square.
Extended each line of the square approximately 2 inches in both the horizontal and vertical direction. (see drawing)
Placed my feet parts on the extended lines.
Measured and cut my conduit for each axis. I found that the calculator was within 1/16th of an inch of being correct. (mine numbers were a little short)
This resulted in my overall "out of square" being 1/32nd of an inch across 2 feet in on both axis. This might have been luck, but I hope it was my skill. (lol)
And then you need to check the corner pieces, you can be off a little from the feet. So square the top and bottom (you can even check top to bottom but that is excessive).