My recently procured 2003 EB was a rattle-trap like I’ve never heard before. And Ford knows it. Turns out there is a TSB that (under warranty) replaces all 4 door seals and all 4 door latches. Well that warranty ship sailed a long time ago. I researched the part numbers in the TSB, and it would have been over $1,000 in parts, if you could even get them now.
So here is my solution, and it worked famously. For starters, I moved all of the door latch strikes inboard, simply loosening the 2 torx bolts each enough to tap in the strikes with a punch. Then tighten the torx. The most effective solution, and also the quickest, was to firm up the weatherstripping of all 4 doors. I did this by snaking 5/32” upholstery piping into the weatherstripping. After pulling off the weatherstripping, there are weep holes at the weatherstripping, where I lubed it up with spray silicon, and snaked the piping in. Presto. Doors rock solid, no more rattles.
From Amazon: 5/32" Upholstery Firm Plastic Foam Welt Cord Piping (60 yds)