If you are looking for used, people that buy the rubicons usually dont change a lot, maybe wheels/tires but not a lot. People that are going to do a lot of upgrades usually buy a Sport and add on what they want. Mine was a Sport and I put about $15k into it, now its far better than a stock...
Good catch. Maybe a thin piece of plastic cut to match the rubber diameter, use that a shim? It wouldnt stick to the metal, should take care of it. I'm thinking maybe I'd 3d print something, but not everyone has access to that.
edit: you could glue the side to the rubber so it wouldnt...