Calico,
You are loosing position at a number of spots along the way. So it is not only the roughing. You can see it in the pictures.
I wanted to find the worst / first ones that were causing the gouging and that seems to be in the roughing.
Seems that first gouging accurs, approx, after each 1/4 of code run at a particular depth level when roughing.
So it would be nice to just have that grouping of code to help find the problem, call it a test file.
Then you confirm that there is no error in the code for the Z depth cuts.
You then air cut with the test file and confirm you are not loosing position.
Have a look at the code and make note of approx how much material is being remove and do some manual straight cuts
in some scrap and see if you loose postion.
I think that over a period of time, you are heating up the stepper motor and causing the gouge in roughing.
You could reduce the rough cut depth so the motor is not working as hard.
In the finish passes it's also time related as every 1/3 to 1/4 of the code group you are out of position.
Maybe,generate code for a piece half the size and depth and see what happens.
Maybe someone can be more definitive.........
RICH