Almost a year later, I found my rattle. The rubber piece that connects from the frame to the body inside the wheel well is connected by essentially fancy rivets that appear to have no adjustments. Two of mine had excessive play resulting in metal to metal contact and rubbing. In fact the frame was nicely polished where this wear was occurring.
The solution? I removed the rubber piece, cleaned up the area where the rubbing was occurring, and painted the area. I then added some rubber o-rings to the inside of the rivet to take up the slack. So far, no rattles.
I am curious who has the same issue as me. It appears to have came that way from the factory. Not only does it result in an annoying rattle, over time and in a wetter climate, it would be perfect place to rust.
If you look at the below picture, I had wear on the top left rivet under the rubber (part of the body) and on the frame at the rivet directly below it (can't see in the picture, blocked by the tire).