Well,
Your pictures are worth 1000 words. (though equal parts scary) I'm hoping I don't find the same amount of rust, but with the '05 EB 4x4 with sunroof (that leaks), I'm expecting things are not too pretty. The issue is we live in a heavily wooded area with Pines, Oaks, Elm and about a hundred more varieties of native trees. For all the good Ford put into the gen. 2 Expeditions, there were a couple of ... exceptions. The grill keeping the wiper-well debris free and the sunroof drains are two prime examples.
While the plastic grill over the wiper-well is easy enough to remove and clean under, the areas where it meets the A-pillar and then down the sides behind the door hings are almost impossible go ensure are free of debris that could block the drain-path. I hadn't even considered the C-pillar route until your pictures for the rear-drains.
The plastic grill over the wiper-well is course enough that it lets all matter of oak leaves, acorns, acorn (whatever you call the part of the bud that holds the acorn while it's growing) and pine straw pass freely through. Driving disperses the debris across the entirety of the well and down the sides into the A-pillar area. The wife parking under a large oak at work every day only exacerbates the problem.
Thank you for your pictures. Finding a good diagram of the drain routing and any cleaning procedure (other than running weed-eater line down the drains with liquid-plumber to clear any blockage) has been elusive. (I'm not sure I'd want the liquid-plumber touching any of the plastic or rubber parts of the drain-lines). Your picture and description make clear with the lines stopping behind the sheet-metal and debris in the area also being a problem shows the lines themselves are only part of the problem.
I've judicially reached behind the door hinges into as much of the openings as I can. (using a 18" bamboo leaf stem (not the main shoot, the side shoots that the leaves grow on) makes a fantastic paint-safe probe less than 1/8" in diameter on the small end, that is rigid enough to dislodge most of the leaves, acorns and pine straw that can be seen. (a lot of it is just mulch at this point adding to the challenge)
If you have any other pictures or advise on your panel clean-out that may. in any way, be considered helpful, please think about adding them to your post. This is by far the best collection of sun-roof leak cause and effect information I've found, and I've looked casually for the past couple of years. Even TSB 08-24-8 about the leaks when running vehicle through the high-pressure car wash doesn't provide detail on anything but the rear trough seal.
May also consider adding "Rusted A-Pillar (leaking sunroof)" to the title of the thread so that causality is clear in the title. I think that's likely the reason I hadn't found this until joining the forum.
Thank you again for collecting and posting this information, it is read and appreciated. I'll keep a blow by blow of my encounter with the panels and try and do likewise.