Tonight I went out and did some blocking with the intent that if I sanded everything off then so be it. Instead what happened is it ended up revealing the high spots really well. I took some pics for your guys' input on how to deal with these. I could tap them down, but since I can't get access to the skin underneath I can't put a dolly there to push up on a low spot. I also stuck the scoop on so you can see where it will be in relation to all this.
The little high spot with the dime sized bare metal spot is indeed near a spot where the skin is glued to the frame, though it's not directly over it. I'm only working on the passenger's side right now.