hmmmmm, it sounds like the lip inside the wheel well, that cant be seen until you get
below it and look up?
if they replaced the rear quarters or just the quarter skins,
what you might be looking at is a botched welding job. some body
shops will let a novice do the welding in places it cant be seen. if this is the case,
spray the area with your garden hose and see it water gets into the trunk. if it does,
ya gotta fix it. usually you can use an asphalt type undercoating.
BUT....
if it really is rust, you gotta cut it out and replace it.
a friend of mine replaced his wheel wells on his 67 gto with one from year one and,
was very happy with the fit. but, he said they were a lighter guage than the original
ones that he took off.
hope this helps,
dallas