I would think there would be some kind of drain tubes to help get rid of some of the water under the cowl, but I'm not really sure. I've been meaning to remove it and clean the decade of pollen and leaves out of there but I just haven't had the motivation to do it. Maybe I'll pull it this weekend if the weather holds out.
lol
Update on the search for my water leak. No luck yet on the source of the water leak, but I did get a photo of the moon roof drain holes, removed the windshield cowl with a photo of it removed and how to remove the windshield wiper arms. I started by looking for the moon roof drain holes with the moon roof opened up. There are no drain 'slits" as another poster mentioned in another similar topic for water drainage, they are round holes instead. There is one on each side of the moon roof, in the "front corners" in the underside of the framework for the moon roof. They look like black holes as you will see in the photo below. Look for the black hole in the corner of the moon roof, that is the drain hole for that side. There is another one on the other side of the vehicle. I ran a foot or more of wire down the hole and both holes appeared open and clear to the point where my wire hit the bend for the A pillar and the tubing started to bunch up on me at this point. The wire I used was a soft core wire(all I had) and would only go down the hole so far till it started to bend up on me. A stiffer wire would be better to reach the other end of the drain tubing.
Next I removed the windshield wiper arms, which were extremely easy. My wiper arms have the small spring loaded "lever" located near the pivoting knob that the wiper arm is attached to. To remove the wiper arm, fold out the wiper arm away from the windshield, then rotate the small lever arm outward, holding it in place and pull or pry up on the wiper arm and it should pop right off the pivoting knob. You can use your finger or small flat head screw driver to rotate the small lever arm. Re-installation is reverse of removal just be sure to re-install the wiper arm in the same location on the pivoting knob as before so it clears the windshield properly when you go to use the wipers and so that it returns to it's normal out of the way resting place when not in use. Leave the wiper arms off to remove the windshield cowl.
Below is the photo of the windshield cowl removed. The cowl is one piece that is held in place by upper and lower clips that snap into place in slots, similar to the inner side wall panel clips inside the truck. I started removing/ pushing up on the cowl clips at one side(by fender) and worked my way towards the middle as far as I could go on that side. Then I went to the other side and started prying up on the clips at that end working my way towards the middle, then I lifted up on the cowl to pop off the clips in the middle. I had the cowl off in less than 5 minutes using just a flat head screw driver and a windshield removal tool I have. One or the other can do the job. To re-install the cowl, it is reverse of removal and it snaps back down into place just using your hand/fist to pop it into place.
As far as my water leak, I found no traces of water under the cowl, in fact, it was bone dry under there and it rained again last night and I saw no drain tubing running through there at all. Rain water appears to drain straight thru the cowl (near the center) to the ground under the vehicle. Base of windshield seal appeared okay as well. I'm stumped at this point as to the source of my water leak. Sorry if the photos aren't that great or if they don't come out at all, new to this photo linking stuff.
Edit: I think I figured out this inserting picture stuff into posts from Photobucket.com