2004 Expedition Sun Roof Leaks

How wet is the foot well? This is likely to be one of two things. Door seal rubber or the Heater matrix.
Try this bit of detective work. Does it only get wet when it rains heavily? Is it just the front that is wet? Feel the carpet in the foot well. How high up the foot well carpet does the wetness go? Does the wetness smell of anything? Do you have a sun roof fitted? Sun roofs have drain holes that can clog up so the rain pools up in the grooves and runners then over spills inside the vehicle.
If it only gets wet after rain it could be a worn out door seal rubber or the sun roof letting water in. Door seals usually cause shallow pools of water so the wetness won't rise very high up the carpet. The sun roof sometimes causes the seats to get wet as well.
If it is wet all the time, the wetness rises high up into the foot well and it has a 'sweet' smell, it could be the small radiator unit,(the Heater Matrix), behind the dashboard that supplies heat to the heater blowers leaking. Depending on where exactly it is fitted you'll sometimes get wetness in both front foot wells. The smell is the coolant from the engine.
Hope this helps.

Body leaks can be a nightmare to find as the ingress point is sometimes well away from the wet spots.

Door seal, sun roof, sun roof drain(s) and windscreen are the most common ingress points though sometimes a blocked heater drain can cause a flood especially if the car is not parked on level ground.

drain pipes are blocked due to which rain water is not removing by self, u need to use high preasure compressed air to clear drain pipes located on both right front sides of sun roof.

once blockage is gone, then u wonr face this water logging issue

One side only or both? Do you have a sunroof? Clogged drain vent for sunroof, cowl, A/C, bad weatherstrip?

Start by cleaning the junk out of the sun roof drains. Don't poke anything down, use a vacuum.

And where exactly is this rain coming from? The sun roof? The door seals? Seeping in down in the footwells (soggy carpet)?

Sometimes "rain" can be mistaken for A/C condensate that is not draining due to a plugged condensate drain. If your A/C is running and it's hot and humid out then you should see some water drips on the ground underneath the front area of the vehicle. Let it sit in one location for a few minutes after you come in from driving it. Let it sit for a few minutes with the engine and A/C running. Move the vehicle and look for the telltale wet spots from the condensate drain. If you don't see a wet spot then chances are the drain is plugged. The condensate will back up and drain inside the car ...typically in the passenger footwell and making the carpet wet.

Sounds like the door gasket or trunk gasket is not sealing.
You may have to take it to a body shop to find the problem.

Do you have a sunroof?? you are probably leaking at your sunroof if you have one... sometimes the seals just wear out it is a common problem... you can go into a shop and ask if they can take a smoke machine to it and see if they can find it...

Sun roof drains are clogged

Great solution: Use a 8 foot length of weed eater plastic "blade". You can get a small amount from a hardware supply store. While twisting the strand, insert it into your drains that are located in the corners of your open sunroof hole. Feed the plastic thru the tubing... don't force it, use gentle pressure. Test with a bit of water and look under the car for drainage.