Without the middle assembly in place, the gantry is square. I pulled everything apart and started adding the middle assembly parts back on piece by piece as suggested. With just the middle joiner parts in place everything goes out of square.
So I’m going back and trying to re-calibrate the printer for PLA. 20mm cubes are coming out around 20.3mm. I don’t seem to be over-extruding (e-steps are right, and I keep dialing the extruder % back), so I’m trying to figure out what’s going on – but I’m guessing this slight oversize is causing the issues.