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Ok, Thanks that was very nice

That is a PCI card (a 5I20)

If the motherboard is OK, probably the easiest path
is to just get a new harddrive

Is there any chance the original HAL and INI files  are available or
can be salvaged from the hard drive?

One thing on the plots, adding the Z velocity would make analysis easier.
Both in determining the start of motion and the point where Z motion
becomes synchronized with spindle rotation

Also an actual screenshot is easier to check than a picture because its
accurate and does not have geometric distortion. (making it hard to tell if
lines are straight)

Here's another interesting example. I first made a threading scratch pass at 50 RPM. When the second pass started, I cranked the spindle speed quickly up to about 300 RPM (I'm guessing), then back to 50 RPM. The second cut started overlaying the first, then went to the right as the speed increased, then back to the original cut at the end.

So the speed definitely affects the Z position, and my original concern about the lathe bogging down during threading in a deep cut and then that slowdown causing gouging is warranted.