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I was applying silicone spray to the rubber on my door frames today (as instructed by a Ford mechanic to keep them soft and quiet) and I noticed a small rubber tube stuffed above the latch for the rear door. The one on the drivers' side almost fell out, but the passengers' side was glued in there. It seems like a cheap fix for a wind or water leak. Anyone else seen this? Does it need to be there? I may re-glue the drivers' side, or just take it out and see what happens. I could take a photo and attempt to post...
My 99 4dr has them, I'd thought the same thing when I first noticed them years ago, they almost seemed to be someones after thoght to a sealing problem. Just exactly what they're supposed to accomplish, I don't know, but both right & left sides of mine have them.
If you've sprayed silicone on the area to be bonded, it won't be easy to remove, but you MUST remove as much as possible, bfore attempting a rebond, lest the silcone will corrupt that bond.
Try calling your local Ford Dealers body shop & see what they use to clean & rebond those door seals.
Let us know what you find out & successfully do it with.