Damn. I have the same problem. First noticed it a few years ago, but it mostly rains a few days in December in SoCal. This year we've been slammed with a few weeks of steady rain, hard at times.
My driver's and passenger footwells on the drivers side are completely soaked. The door sill channel that the rear wire bundle is in was full of water (I park on an incline at home) so I had to remove a body plug to drain it.
Today I pulled the driver's seat and the rear seat supports and raised the seat bottoms out of the way so I could lift the carpet and dry out the pad. Got a small space heater and a fan in there now, with the windows cracked to relieve the humidity.
Saw a few drops on the ebrake cable housing.
Last night I did a quick leak test by pouring water on the roof. I poured water in the strengthening relief in the roof at the windshield. Saw water travel down to below the windshield in the cowl/wiper area. Weird.
Also noticed that the front door seal was tweaked...not sure if that's an issue or not. Used duct tape to force it back to its normal shape, as rain water travels along this seal.
Sucks the way Ford designed it so this seal dumps the rain water on the door hinges and that main wire bundle holder in the door jamb.
I spread some silicone along the top of the door hinges, just for the hell of it, to try to get the water to move along and drain properly.
I put a high intensity light in the driver's footwell, but couldn't see any light from the outside and underneath the truck.
I'm going to order all new door seals and the hood seal.
I wanted to upgrade to a Navigator or loaded Expedition, but the current economic crisis hit us hard. So, I gotta pay extra attention to extend the service life of my 145,000 mile '99 4.0 SOHC Exploder