I finally finished installed a front door....and got back to checking the X and Y gibs. Pretty easy to remove and re-install.
The gibs seemed nicely machined. No noticeable burrs. I did a very small amount of rubbing with same sandpaper on a granite plate to be sure I wasn't missing any burrs and reinstalled them. However, I'm not sure how tight they should be. They seemed quite loose and I made them a bit tighter. Suggestions on how to judge gib tightness (preload?) would be appreciated.
After putting the gibs back in place, I re-measured the perpendicular-ness between X (long side of square adjusted parallel to X axis) and Y. Not much change from the first set of measurements. Over 4 and 1/4", I was out .002" (.052 mm). Very close to the same amount off as with my first set of measurements.
I've found that it helps if I think about the table being .01" out of perpendicular over the full length of the X axis (24"). Seems smaller than 1/4 mm.