Hi @SeniorCutMaster,
This was briefly discussed in this thread, in relation to the release of GRBL 1.1H version, and how it now supports “Dual motor support for self-squaring gantry homing”, which is exactly what you propose.
I took away from that discussion that…unfortunately, the Shapeoko controller board won’t support that, you would need to upgrade to another controller (doable, but not a piece of cake, so worth thinking twice)
Also, in my opinion you should rather invest a little bit of time to get to a good squaring of the machine than trying to compensate for it being out of square in software (3D printers are different, there is virtually zero force applied on the tip of the extruder). I have a feeling that even if you installed a double Y switch, you may still have to fight other geometrical inaccuracies of the machine, because the “twist” may not only be on the X/Y plane.
Last but not least, can you share the repeatability error value you are seeing ? Some people here do precision work, and it should be possible to dig up “reachable” values on a square machine with proximity switches in earlier posts.