For some reason, I wasn't notified of the replies to this thread, so I never saw any of the suggestions! Thanks everyone.
I ended up getting some 400 grit w/d sandpaper, putting it on a block, and knocking the pickup top down level again, then giving the surface two coats of lemon oil to restore the black color. It took less than 5-6 minutes to do both pickups, and they look brand new now.
Even if the marks will come back eventually, there is something nice about putting a new looking set of pickups into a new bass.