I'm not sure which machine it is that you have, but i was just thinking, if its built like mine, the griz x3, there is the potential for slack in the z axis ways, so, in my mind, if theres slack in the z you might tighten the jibs a little and see if that changes anything...
if the head is pretty solid with the column, then it sounds like the column is not plumb..
.002" over .500" is an angle of .23deg. so its not much.. way smaller than anything than i can measure.
ok, so i'm going to ask this next question, cause its something that poped in my head, and i havent had my coffee yet... is it possible for the work peice to not be flat down against the table, could that cause this angle gouging?
Grizzly X3, CNC Fusion Ballscrew kit, 3 500oz-in bipolar steppers, 3 203v Gecko's, Linear power supply from Hubbard CNC, Mach 3, BOBcad Pro Art V22, Rhino.