So,
I have a great update. I got the machine working. Using the X-minus hall switch did not do the trick. Testing everything that I already thought was not the problem gave me the solution. The magnetic linear encoder in the X axis was the problem.
I did most of the testing of it at low speeds and short distances, as my indicators obviously cannot measure the length of the full axis. I can remember doing a test running the whole axis at rapid speed for multiple minutes, but I may have done this only on Z, it was two weeks ago. Or it got worse somehow, I don’t know.
In the end, using the motor encoder resolved all the problems.
I also disassembled the X axis to see how the encoder is installed. There is a very small read head in the plate behind the thrust bearing for the ballscrew and a putted scale in the underside of the X-axis slide.
I also made some pictures of the Z-axis encoder.
And then, after I spent all day getting this done, I was able to actually make op 1 on the test parts I wanted to make as test parts.