I helped my Dad last Thursday (10/24/13) with a leaking sunroof in his 2006 Ford Explorer. Apparently this is a common issue that Ford never offered to cover for it’s customers, and they wanted $600~ to fix the leak for my Dad. I was able to locate a DIY fix from a former Ford tech, and I have posted the pictures and details below for others to view.
The text in the picture above reads “Where the space is between the roof and the sunroof frame place the Duct Seal in this area to keep the water from splashing over the top of the forward edge of the frame. Place the Duct Seal from the center out to the edges on the left to the right but not covering the drainage holes. Arrows point out where to insert the Duct Seal.”