Glad you found your major problem. I had the same issue but it was showing itself as missing steps. I found it by accident when I was taking it apart. Ran the slide forward to take the screws loose on the stepper mount plate and they were so tight I had a hard time getting them loose. Ran the slide back and they came out easily. If yours set for a long time with the slide in a location to exert that much pressure it may have contributed to the warp. How about removing it and baking it in your oven for a while then letting it air cool? It may relax and release the built up stress and self level itself.

Your discussion makes me think of the other things I've resolved since I got my machine in 2017. I'll briefly list them and their cures:
1) Z axis max speed was very slow - idler pulleys on drive belt needed additional clearance to rotate freely and one of the air springs had failed.
2) Excess end play in X axis - clamp nut on leadscrew (by tailstock) came loose several times (always worst possible times). Increased gap size to allow increased clamping force.
3) Mill spindle running in reverse direction than commanded - switch 2 wires feeding motor.
4) 3 connectors for limit switches on back of controller not being recognized by Mach - ground was connected to machine ground, not to 48VDC zero voltage. Gecko never sees the signals. Correct wiring so connectors see Gecko ground.
5) Overall differences in accuracy - Tighten all encoder mounts, verify and correct DRO calibration as needed (do this first when setting up your machine, please!)
6) Loud clunking noise in X axis handwheel area - excessive backlash in handwheel gear train. Shim as needed to remove.

I'm sure there are others I have forgotten. But in the long run, would I do it again, YES! I have worked in places with very expensive equipment and had similar experiences.
I bought what I could afford and fit in my location. I didn't expect it to be perfect, but it gets closer each time I use it......