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Nice class there brad, couldn't have explained it better. If you replace the entire panel there will be no visable panel overlaps to deal with at all. You drill out all the welds that hold the original box side on, there are about 20 on the inside lip inside the box, a dozen or so down the front where the side meets the front wall, a few inside where the tilgate hinge is located , a few more underneath the rear quarter panel that most will forget on the first try and then a couple more where the wheel arch meets the inner fender. When you are done you will only need sand, reprime and paint the panel. With good tools and patients you should be able to remove the original panel, prep where the new panel bonds to the old by removing any paint or rust, bond the new panel and have it ready to prime in about 6 hours, less if you have some experience. The worste is drilling all those welds out, bring some beer for that part.
see that's where I was not on the same track --- I wasn't thinking replacing the entire side panel of the bed - just the section that runs top of the bed to the bottom edge from a few inches in front of teh wheel arch to just the other side of the fuel door --- it doesn't seem like this option would work all that well for this situation -- or am wrong again ... I say that mainly because there would always have the that edge to deal with and reducing the profile of the wheel well
if it were the entire side of the bed this seems liek an outstanding option
You can panel bond repair patches as diesel brad showed above. You can also buy a step tool that puts a "step" in the repair panel that makes the panels almost flush when either welded or bonded together. This is where things do change, if you are going for a show look and finish then the longer harer route of welding and filling is the way to do this. Panel bond will produce a small shadow that is hardly noticable if done right, that is caused by heat expansion in the metal. If you are building a daily driver you want to look good but not perfect then you can go ahead and panel bond the repair, if you want perfect you will need to weld in the panel or replace the bedside completely. If you are keeping the truck for a long time, replace the entire side and it will never need to be done again and you won't have a bondo buggy either. By the time you weld, fill ,sand and acount for your time , the replacement side is cheaper.