Ok there's a few things going on here. Most modern vehicles are built with tight tolerances so there's no shims or elongated bolt holes. If body panels are scraping each other something is bent somewhere weather it's a " messaged " body panel or part of the inner structure.if you see shims or elongated holes anywhere on a 4runner something is wrong.
Most likely you have a fender that has been messed with and it was deemed " that's good enough ".

You say fuel cap, do you mean fuel door? Those can bend from use. I've had 2 4runners that that has happened to both with new fuel doors. You can do small bending of the hinge to get them back right.

I would definitely get that frame rails checked. It can cause alot of issues if it's not right. It can cause suspension premature wear, rear steer, other body misalignment. Frame damage at a trailer hitch can transfer damage to other places on the frame as you have reinforced that area stronger than intended. Frames have crush zones on certain areas so that area has been strengthened due to the hitch so damage will transfer to other areas away from the hitch. Even though some 4runners came with factory hitches as an option, the frames remained the same.