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Well surface or gone through? no matter what you will have to replace them with new metal cause it will just come back fairly quick and spread lot of online sites like lmc truck and in the sponser list will sell wheelwell panels and whole bed side panels or a body shop would sell body panels
Of course you could do it yourself for cheaper and get the metal from somewhere but I would check with a bodyshop for a quote its not cheap these days especially if you got two tone paint
Depends how long you're planning on keeping it. My body guy advised original metal lasts longer than patch pieces and after time you can see where the patches are. Used rustfree box will run you $900-1000 (depending on where you're getting it from). Check with a body shop for after market replacement fenders and cab corners. Mine is still in the bodyshop so have NO IDEA what it's costing...
www.LMCTruck.com has prices but not sure how they compare to local vendors but it should give you a ballpark figure.