Ryan, I am at almost the same point with my renewed machine. All bearings are in touch, the whole construction seems to be much more ‘on the point’ than the very first one, see elsewhere.
Today, I measured the angle of the X-Y-gantry rails, first completely unloaded on a desk, then put loosely on the rollers. Same result, the angle (measured in the quadrant where the tubes meet directly, see from above) was 90.7 degrees. Controlled playing with bolts A and B led to results between 91.0 and 90.5 degrees. Whatever combination I tried, I could not get below that value. The two A boltes are so loose now I can turn them by hand. Snugging B to the limit (no cracking sound yet!) did not really change much.
As I use Linuxcnc to control the machine, there is a theoretical solution, but my Linux- knowhow reaches its limit on this too quickly to let it look like a practical workaround:
Shall I go the empirical instead of the deterministic way and disassemble everything again?
The parts were printed on an alfawise U30 which I triple-checked for squareness. PETG.
BTW, the 130mm bolt can easily be replaced by a 120mm one. Less protrusion, more pleasant to the eye.