So I decided to disassemble the MPCNC and assemble the gantry from the beginning. The first thing I checked was getting the middle rails parallel without belts and the middle assembly. I noticed right away that the middle Y rail would not stay parallel to the outer Y. My X and Y lengths match, and my diagonals are within 1/32″ so I am guessing that one of my Rollers is slightly skewed causing this issue. I tried the bolts really loose, just snug, and tight in all the various arrangements (inner bolts tight outer loose, flipped, at diagonals, etc.) and nothing made a difference. I am thinking some sanding is in order to get this parallel and start from there.
I also made some “squaring arms” for when I put the belts on to make sure I do not skew it then as well.