I'm 100% certain the damage is from the wheel well hole. There is too much evidence that supports it. The slopes in the sheet metal in the trunk, the dirt build up and dirt trails. The damage is a lot worse than I thought. I'm going to get some auto body quotes today. I'm expecting this to be an expensive repair.
Inside. Strut appears to be fine, no rust damage.
Dirt under the seat (and enough change for Taco Bell) Guess this is the reason why my car smelled so gawd aweful on the inside.
Going to Toyota (formerly Pontiac) to get a quote. Then off to a couple body shops and then to Snell (New Pontiac). So far the lowest quote I got is $92, the highest $160. I think now that its all visible it'll be a bit more. :(
Thanks for all your help. I wasn't even expecting to find this hole. It was pretty well hidden.