Just an update for if anyone cares, those lines cause in the work piece is actually from the dust boot being too low. I haven’t had any similar issues lately and barely made any adjustments to the machine. I just dropped my dust boot down yesterday, and had the same effect!
I’m not sure why this would cause all the wonkiness, I presume it would be because of too much pressure between the work surface and the gantry etc. (I know this doesn’t specifically affect the z-axis)
Brought it back up, resolved the issue. Hope this helps someone else who might experience it.