I have a 2013 XLT 5.0 that I bought a little less than a year ago. It had cheap fender guards on it and the left front one came off driving it home from the dealer.
I called them and the sent me a new set. Upon removing the rear left on I realized why it had the guards on. There was a rust hole about the size of e nickle just above the wheel edge where its quite thick.
Paint is bubbling an inch around it now. Took it to one repair shop and was told he would have to replace the whole outside side panel to keep it from rusting further and it would be around $3200.
It there not a way to repair that area properly and not replace the whole panel which is spotless other then rust area?

 

$3200 seems high to me. I had the drivers side bed panel replaced and painted along with a new bumper on a 2010 for around $2500. I’d shop around.

 

Wonder how much difference an OEM part panel makes vs a third party replacement panel?

 

Don’t buy new body parts. Plenty of body panels in junk yards.

 

The repair shop is right, to repair that properly to prevent rust it is best to replace the panel/ bedside. Also if he knows what he's doing he will bond instead of weld in key areas to avoid creating more areas for rust to form. Assuming he's using an OEM panel the price he quoted is fair. Of course you might find it cheaper at another shop but in body work, you often get what you pay for. Rust sucks and its expensive to repair correctly.

 

You might also consider replacing the whole box with one from the southern states. May sound extreme, but the other side probably has similar rust hiding, just waiting to bust out. The boxes are available and while you have to paint the whole thing, you are starting with a solid base.
Patching the rust is something I did for years - until I sourced a rust free box. It was the only rust I had and the truck was 29 years old but still running and looking great.

 

This is a solid suggestion.

 

2010 to 2013 have that problem, I have a 2013. The reason why it is rusting is because of the stupid ford engineers. The fender is double wall and seam weld at the meeting point. The trucks rattled a bit. So the brilliant ford engineers applied a picky size bead of silicon chalk on the seam. Water sits on that spot and between 6 to 8 years the rust starts. Only the rear fenders. Actually from the back you can fit your hand through the opening and actually pull out some of the silicone foam crap. I have this problem too.

 

I do not know how far out on the Cape you live or how long you have lived there but once you pass the Cape Cod Canal the price of everything goes up so out there that is more than fair.

You do not live in the Rust belt do you? Go to the wrecking yard in New England and the parts you find body wise are just as bad if not worse than what you are trying to replace. Just Saying.

 

Any junkyard worth using is connected to every other junkyard worth using. They can order the parts you need from another “non rust belt” junkyard. There is a wonderful world outside of the rust belt.