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Well I finally squared my X and Y axis. It didn't work out quite as expected and the left of the front plate of my Y-axis is now raised off the table about 1mm, but appears to be working properly otherwise.
I thought I would document what I tried in case anyone has feedback that may help me or comes across the same problem.
I tried a few things to square it and they didn't work out quite as expected.
Method 1: Loosen frame, measure align and re-tighten each part of the frame
Using the first instructions of squaring all parts of the frame loosening bolts and re-tightening didn't really help. I had a few problems:
1) Measurement accuracy is difficult
I tried with tape measure, ruler, vernier calipers and string for different parts but I think there was still at least 1mm measurement error just trying to measure parts of the frame on the diagonal in particular. I considered super-gluing sewing pins to the frame to give accurate posts to measure between with string but didn't get around to trying that
2) After aligning everything I can get it to look ok, but then tightening it up and it just goes back to non-orthogonal
Method 2: Adjust just Y-carriage bolts
I then tried the idea of keeping the frame as it was tightened (and potentially unaligned), and just playing with adjusting the Y carriage bolts. But every time I tightened up the nuts on the M8 rod (particularly the rear ones), they would become perpendicular to the rear frame and non-orthogonal to the main frame/x-axis again.
I "think" the problem is that somehow the rear frame that the Y-Axis attaches to is not perpendicular to the main frame. I couldn't see this with measurements (measurement error) but was a hunch.
Method 3 (kind of worked): Space out rear frame
In the end my solution is not great and I wonder what other consequences it may have going forward.
I spaced out the rear frame with some plastic on one side (see attached photos).
This has also resulted in a problem I had earlier where the front right of Y-carriage (that sticks in front of the machine) is now raised about 1mm off the flat surface (See other photos where I have red plastic under it).
I used to have this same Y-axis problem where front left was raised 1mm off the bench and it was causing "grabbing/shuddering" of the bed as it moved in +Y direction. I am not seeing that now so maybe it is ok.