Hey Travis,
the best thing would have been to search the forum for squaring. As of this writing, the first hit on the search is → this thread from the other day, which deals with rectangularity (“squaring”) of the machine and leads to other threads on the topic.
See also What do I do first – Post #6 by Aiph5u
The key to a squared machine is to first lay out the squared geometry for the holes with a punch, drill the holes and only then assemble the machine.
Best is to rely on the individual measurements made from your machine since the dimensions in the manuals could be not 1000% correct as sometimes the anodized aluminium blocks could be a very little off on the chrome-plated steel hollow shafts. Possibly if the distance between the front and the rear anodized aluminium block is not identical on left Y and right Y rail, you may adjust that first (with the rail on a granite plate), so that the squaring by ensuring identical diagonals works.
By the way, I would not recommend to use the screws for the feet that are delivered with the machine. It is better to use bolts instead. Here is the cross section of a Onefinity CNC foot:
Repair hole: If you have a hole in wood that is not at the correct location, you drill it out to the next larger diameter, glue a cylindrical wood dowel into it, let the glue dry, saw off the excess with a flush-cut saw (dowel saw) or a Kugihiki, sand it, and repunch.
Imagine you mill something that is a rectangle. How much do you want the side not to be square to the front? 1/10th" after one foot? Or imagine you want to mill a wooden box with a wooden lid. How square should it be so that the lid fits? If the box is a parallelogram instead of a rectangle, because your machine is not squared, and you milled the lid upside down (which would be logical as its pocket is on the underside), the parallelogram would be in the other direction, and the lid would not fit. It will only fit if the machine is squared.