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I fixed mine also. I cut off the inner lip of the door panel (the door skin that is folded over) this is where all my rust was. then I used some POR 15 on the inside of the door and on the removed rusty lip. I then used some 2 part epoxy/ filler to smooth out the removed rusty metal. I then used some high build (durable) stone/chip guard to paint the lower 2" of the doors. I have some pics and I will have to dig them out. It`s going on 2 years and they still look good with no signs of rust forming again!
BTW, it`s not just Ford. GM has the same problem also.
I have the same but worse problem on my 2000 XLT Ex. Someone already did a cheap repair.... Now my doors are gone at the bottom. I could replace the bottom inside and outside, but I am searching now for a pair do replacement front doors... I think that will be better and cheaper in the long run.
I fight this yearly with 6 months of salt on the roads. Once the repair is done coat the inside of the door with por 15 and then spray it with fluid film. You'll be impressed. Do the same with the rockers and the frame. It ends the problem, period.