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If it's horrible rust, there's always the option of replacing the entire panel. Other than that, you'd want to get some sheet metal welded and blended in if you can.
1980-86 Fender flares look wicked on the later trucks if you wanna save money. I personally wouldn't pay someone to do body work as it gets expensive and you will be disappointed most likely. Either it will look crappy when it leaves the shop or it will look crappy when the paint falls off.
Not to hijack a thread, but I have a similar question about rust. Well, sort of. My Bronco doesn't (at least that I remember) have what I would call the "typical" wheel well rust: eaten through so you can see daylight within the first couple of inches of metal around the wheel opening. It looks like someone just shaved off the edge of each wheel well. I mean, almost like you took a knife and cut off the straight edge of a cardboard box, maybe a 1/2 inch? The opening isn't big, but when you get up close and look at it, you can see the painted quarter panel and the inner wheel well metal are about 1/2 inch a part and there is just open space on all 4 wheels. WTH?
My question was going to be I assume I need to do something or this is going to rust... I assume the "proper" way to fix it is to replace the metal. If I leave it be or cover it with fender flares, how long is it going to take rust (in Kansas) from taking it over?