This thread is three months shy of 5 years old so I am going to hi-jack it. Every time I searched for passenger water leak, this thread came up. From the research I did on this and other forums, I would agree with Marcus. Here is what I had on my passenger floorboard after a decent rain.
My cowl had only 1 screw out of the FOUR that should have been holding down the cowl. My car is a 1998 so it is 18 years old but well cared for. I took the cowl off and noticed the air inlet was only slightly cracked on one side and appeared to be the original seal. I had some black caulk that was opened and needed to be used anyway so why not take off the air inlet and see? I started to pry the air inlet off.
As Marcus mentioned above, there was nothing of interest inside the air inlet. Now I couldn't see well inside but nothing jumped out at me. From research I learned there is a foam strip underneath the cowl that I thought would be disintegrating and needed to be fully replaced. I also knew I would need to keep that cowl pressed tightly against the windshield. I ordered the clips and screws. The clips and screw closest to me while I took the picture are the original (or at least what came out of the car) and the others are the new pieces.
Once I took the cowl off, I discovered the foam strip was in good shape but the problem seemed to be it shrunk and moved downwards over time. The loose cowl along with time I feel allowed the foam to move thus water could run to the bottom of the windshield then onto the metal where that foam should be and 'bam', into the air inlet. If your car is standing in place like mine was while at work, all that water simply runs down into the inlet.
I took some black caulk, taped it down and kept pressure on it overnight. The next day the foam was where it was supposed to me. I test fitted and didn't need the foam I bought but I cut some pieces and placed it just below the windshield as an extra buffer. If water does get past the factory foam, I have a bit more just past it. It may work, may not. Too soon to tell until the next serious rain. Here is a picture of the foam I ordered but it is too narrow to use if I were to replace the original. For you people out there in Mark VIII land needing to replace the foam, I suggest getting a size twice as wide as what I did. The thickness was the right size though.
I put it back together with the new screws and clips (no pictures) and I will let you know if I have rain water in the passenger area.