When in doubt, always remember, in bowling reaction, SURFACE is king.
By all means, do change the surface. Going to a 4000, or even lower, is definitely going to smooth out some of that over/under.
Dulling it down may mean that you have to play a slightly more open shot, but it will make it read a bit more oil without over reading the dry like it has been with the polish on it.
Really shiny balls, especially ones with a weaker cover to begin with, give me fits with over/under. My pearl misfit was JUNK in my hand til I hit it with a scotchbrite pad, now it is pretty good on the really dry stuff.