I here ya on taking the box off a Ford mostly with rust. I don't know how many torx bits I wasted trying to get the bolts out.
On the old Chevy's we would leave the inner rockers out and just replace the outer's so they couldn't hold moisture again, never tried it on a Ford.
I can see why it rusted. I huge gap where the rear tire is throwing everything at it. I'm just gonna por 15 the inner. Its actually the reinforcement. The inner is still there. What a mess.