Fix for Rusty Rocker Panel Problem.
My 1991 Explorer had the rusted rocker panel problem too. In 1993, Ford covered the rocker panels up with a plastic or fiberglass skirt. That protects the rockers and lower door from rocks, but it did not fix the rust problem on the rocker panels (although it does mask it for a while so it can't be seen).
The problem is with the internal construction and the failure of Ford to seal the seams between spot-welded panels. With the internal construction of that area of the vehicle, there is no way to rustproof that area of the panel. There forward rocker panel goes behind the rear one all the way back to the wheel well . . . with only a small fraction of an inch between them. There is no way to rustproof that. The two panels are spot-welded together, but the seam you see below the back door is not sealed. Moisture (and salt for those of us in the northern climites) travels right through the seam. Similarly, the seam all along the inside of the wheel well is not sealed, so moisture gets in there and runs down into the rocker panel. It is inevitable, the rocker panel will rust out.
What can be done?
The dealer can cut out the rusty metal and weld in a new panel. This, however will not solve the problem. The problem will return, just like fantasygraybear experienced.
Another approach is to replace the panel with a fiberglass panel. That's what I did. Both of my rocker panels are now fiberglass. I now have one of the few 91 explorers in this area that does not have rusty rocker panels.
Where did I get the fiberglass rocker panels? I made them. I created a mold that creates the rocker panels.
I cut the old rusty metal out, sandblasted the area, treated the interior of the area with POR-15, I fiberglassed the new panels in place, and then textured and painted the area. They look just like brand new again. I have pictures of the entire process. I'll be happy to post them out here for you to see if someone will tell me how to do that.