I can appreciate your problem and the difficulty your having.
I had a heck of a time trying to use my mill to do precise 3D machining and could not figure where those steps went or where and when it was skipping.
Like your code there were small increments of XYZ moves and changing from exact stop to CV or any other settings just wouldn't help.
Drove me nuts since the machine otherwise worked well for all the other stuff i have ever done with it.
So here is what i did:
Rebuilt the X,Y,Z axis ....new motors of greater torque, new thrust bearings, and meticulous adjustment of the ball screw nut and thrust bearings.
Now no backlash to deal with and feel very confident on the mechanics and controller side of things.
Now after 10000 lines or more of code at much higher feed rates and rapids, the out of position is .001" at the end of the program.
I think the major cure on my end was the new stepper motors which could deliver the acceleration and velocities required by the program.
Of course the other mods and adjustments provide for repeatable accuracy.
Even though i have the same motors,same gear ratio, same type / make of ball screws, same type belts and timing gears each axis has a different steps per unit
value ( maybe somewhat small but still different ) and I don't find that unusual.
Not saying you need to do the above, but, 3d maching places a higher demand on the system.
RICH