Sorry been hectic and not had a chance to get to the forum the last day or so. I looked at your screenset and tested with your xml but could not see anything wrong and could not get the reset to step the Y DRO as you mentioned.
Looks like you may be making progress though


Oh did se some weird settings for your Jog buttons, but likely you have a reason for that?

Hood

Pray tell, what jog settings?  If they are in the xml they are set by the BOB folks.  I did today check some of the stuff you mentioned.  Every BOB termination was loose.  Not sure what that would do, but in a water pipe it would drip from time to time.

Is there a software fix for an out of square gantry? 

Usually you have two home switches for the gantry, one on main and the other on the slaved side. When you home then the gantry will be squared to the switches.
Hood

It seems out farther than that.  Just messing with the spoil board and framing square it shows out of square in the same direct each time.  I have applied pressure in the direction of correction but that causes the otherwise smooth gantry to rumble.  I need to do some measuring, but it could be out as much as 1/8 inch overall.  I hoped there could be a software compensation.  A mechanical adjustment is not obvious.  I guess having no manual is the bitterness that results from buying cheap stuff.