Mine is an '08. Definitely the clogged drain. When I removed it about a quart of water came gushing out. It was slap full of water.I thought the leaking issues only pertained to the Convertibles. At least the prior post on leaks I've read dealt with convertible's and it was the exact problem. So far, no leaks and I've driven in some pretty good downpours.
My car is a 2008 and I thought perhaps Ford had gotten that issue conquered by time the 2008 came out. What year is your Bullitt?