Sounds like your bed is a lot like mine was when I got my truck. It had some previous PO "badly executed" repairs. I did the fender swap I discussed above and then replaced the back stake pockets with new ones from Mar-K. I also had to rebuild the rear stake pocket holes.
If I may, I would suggest you think aboout how you really want the truck to end up: looking brand new, or looking like a good working truck. I went with the "good working truck" approach. My bed sides are dented, but that was OK for me. Now I can still use the truck without fear of a load shifting and denting something.
It's all good though. Just formulate a plan, or theme if you will, and then try to stick with it.
Here are some photos of what I did for your reference. It took some time and effort, but the results came out pretty good, IMO:
New fenders, old stake pockets:
Drilling out factory stake pocket spot welds:
Old Stake Pocket after removal:
Installing the new stake pocket:
New Stake Pocket Installed:
Stock abused stake pocket opening:
Rebuilt stake pocket opening with radiused bed rails:
