Those pics brought back some memories of when I did mine. My fenders looked the same way. I just cut off the back of the fender and made new angle pieces from an old hood and welded everything up. Can't tell they were ever bad now.
And I too had to cut out many sections of the bed sides too. Just about every bolt hole area had rotted so I cut squares out and welded in new pieces, then redrilled the holes.
ALOT OF WORK!
The easiest part was the tailgate and front bed panel. I replace those with new!
Keep up the good work! You gave that box a new lease on life.
