After a month of rain (13 inches total) I finally had to fix the leak that kept my passenger side carpet soaked. I searched the web for answers and this forum was very helpful. In an effort to pay forward I've documented my repair for all of those who are looking for guidance.
The following photo shows the source of the leak. Debris washes into the crack between the cowling and cowling grill.
Begin by removing the windshield wipers. Pull the wiper away from the windshield and pull the retaining clip down. Then slide the wiper arm off the post.
There are seven screws to remove from the cowling grill. Five on top and two under the hood.
Open the hood and pull back the rubber gasket to reveal the two screws, one on the passenger side and one on the driver side.
Removing the cowling grill will reveal the fresh air intake cover. Debris will build up around this intake cover and form a dam. Water backs up and leaks through foam gasket between the cover and the cowling. Clean out any debris, remove the three screws and lift the cover off.
Remove the foam gasket and clean the gasket seat area on both the cover and the cowling.
Apply a liberal amount of silicone sealant and reinstall.
If you've got a leaky Jeep this repair should take care of the problem. Repair time about 30 minutes.
Aug 3 2011
I've just read through this post, and can see that this repair may not work for everyone. Please keep in mind that in my case, Pine needles and debris were collecting on both sides of the fresh air intake cover, forming a dam. As water continued to flow in from the spot indicated in Pic #1, the debris dam would cause water to backup and leak through the foam gasket. You can kinda see the water line in Pic #5. If you don't see debris on the sides of the fresh air intake, you are probably not having this issue, but you've got to take the cowling off to find out, might as well seal it. I have never (knock on wood) had a plugged center drain. Didn't even know there was a drain. Had I known, I would have taken the time to make sure it was clear. I recommend snaking the drain while you have the cowling off. There are a number of replies in this post that describe that procedure.
Thanks for all your kind acknowledgements.