I've been fighting the rust bug on Missile Storm too from the Duke. I haven't had to strip the CPO (its a very thick stippled paint, no idea how to redo that), luckily there are only small blemished along the very edge. My trackballs looked as bad as yours, I'm looking to get the rollers re-made (not cheap) as they're unique to the Sidams. Keep going, you can do it

One of the Missile Storms is running in attract mode now, pretty pleased about that.
Edit: actually what are the hole fixing measurements on that trackball? While the construction and parts are different, that looks like the same size and bolt pattern as the Sidam units.... I could probably save a lot of money fitting an Atari unit instead of remanufacturing Sidam parts.