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I think I should push out the new beta marlin firmware. I would say make sure the z driver is set to 0.65-0.7V, change the z acceleration to 40 in the firmware (your z is probably not super smooth for whatever reason), make sure your setting are correct in estlcam.
As for not square because of the large build area just do a quick check before every important cut, I measure all 4 rollers form them to the nearest corner block. Each side of the axis should be the same distance. This can get pretty far off if you are cutting in the corner, easy fix.
Your z axis looks really long (seen by the wobbly cuts, or you just cut too deep in one pass), that could also be part of the problem. Cuts should be made at a minimum z extension. Stack things under your cut to raise it up if you need a long zaxis for other things but if you are cutting all the time I highly recommend a much shorter machine. I do this and it can be seen in most my videos, my z axis is about 4 inches (pretty long for a mill/router).
Do some test cuts in HD foam and move to wood, sometimes its easier to spot the issues that way.