I am using R&P for two axis, ballscrew for Z.

Today I swapped one moter/gear assembly, no change.
I then put a tape measure up next to the rack and clamped a small indicator (screwdriver) to the gear area right above the tape measure so I could see exactly where it was.
I made the machine do the usual increments of 5. It was perfect. Right on the money.

Did the same test down at the spoilboard using the endmill as a probe on the tape measure. It was as off as always.
I believe I have confirmed the moter/gears/rack as fine.

It appears that as the assembly slides along the Y axis it must shift/bind/ ever so slightly causing it to rotate and the endmill, being far away from the center of rotation shows the effect by being off by about .100 at the worst point.
thus the spindle becomes slightly out of tram and then comes back into straight again at the ends of the y axis.

Guessing I'll just have to do a lot of loosening/fiddling to try to figure out what is causing the spindle/z axis assembly to shift when it's in the center of the gantry. One thought I had was that the two linear rails aren't parallel enough and the carriages have so little play that they are causing the rotation. I'll try to isolate this by disconnecting the lower set and see.

Anyways, thanks for listening/helping.