Alright, I spent the afternoon removing the rear seat, peeling back the rear carpet and looking.
Turns out I have TWO problems.
This post actually gave me some clues:
The rear passenger foot well was soaked and also under the seat out at the very edge of the body there was a very little amount of water.
There was a lot of leaves and stuff in there, on both sides, so I cleaned it all out.
I never did find any holes like the above post mentions, but I did notice that right at the front of where the seat mounts the seam is open and you can see out to the ground.
The problem in this area is that lots of stuff is sealed with RTV from Ford so it is difficult to tell how the drainage is supposed to work.
What I noticed is that their is a little trough that runs right into the rear passenger floor pan, but there is no way for the water to get out because the open seam is about 1/8 inch high and the water can't really climb over the seam and get to the opening and drain!!!!
I simply enlarged the seam and bent the metal to guide the water out to the ground.
Now when I flood the top (I am talking about REALLY spraying A LOT), the very small amount of water that
collects in there has a place to go.
I did the same on both sides because the other side was very slightly damp, but nothing like the passenger side.
After doing this, I thought about it and reached the conclusion that this isn't a lot of water so how could it soak the carpet even after a few hours of rain?
It doesn't make sense.
So I started looking more.
I put the front end up on ramps because both times the carpet flooded the car was parked on an angle.
Sprayed my water again and WOW!!
It was coming out of the inside of the rocker panel frame (the thing with the holes in it so you can look inside) right at the edge where Ford siliconed the seems.
IOW where the rocker panel meets the floor pan and slightly above.
(you have to pull off the plastic trim to see this)
There was also water dripping out from under the car near the rear wheel, which is how it's supposed to work I guess.
It appears that the water gets channled inside this frame member and exits at the back of the car.
(BTW the plastic ground effects block everything so you can't really see from underneath)
Since the silicone was leaking, lots of water was running right into the rear floor pan.
Also there is a rubber patch over some kind of access hole that was not sealed correctly.
The other side, which does not leak, has a lot more silicone from the factory...
Bottom line, dry it all out and silicone the hell out of it......
I'm going to let it dry overnight and test tomorrow.
I'll keep ya posted