My sizes are out

[Desertboy]

...so the errors are not incremental - so I interpret that as the motor steps, scaling etc are all correct

"Indent is 49mm and the distance between indents is 51mm. They should be 50mm each" - I interpret that that the pockets are undersized?

Post your Gcode output from Fusion. At least for the first two pockets.

Pockets are undersized, here's the code for 1 pocket 50mm in Fusion 360 I had to rename it to .nc to upload from .tap.

my controller is steps per mm

Microsteps are 8, 1610 ballscrew

8*200/10== 160

I have 1605 on Z so 320

1:1 direct coupling.