Get a small sandblaster, mask everything off, and blast out the area. Spray in some etching primer, a coat or two, then paint to match the truck. Then go buy some body cavity wax in a spray can and spray it all up inside the door bottom through those drain holes. Leave out those plastic clip in things from the drain holes when your done. This method might not last forever but it at least makes it look better for a few years. Ford quite using seam sealer on the areas where the door lip is put together/folded over so it's a spot prone to rusting.
'03 XLT/FX4 L1 4x4 4.0 Arizona Beige Automatic (my weekend ride). '16 Ford Escape Titanium ecoboost (wifes ride) '16 Ford Escape S (my work ride)