My 2009 Dodge Ram 1500 also has a leak, but not sure where it is coming from. I have replaced the gasket around the 3rd brake light, no help. After looking at the pictures on the thread, I went with a flashlight to look for cracks and/or water marks and found none. It looks like the carpet/padding behind the seats is starting to separate from the back. I still see no water marks. Is there a way to get the seat back to come forward?
I also think the cracking of the window surround could be related to water not fully draining out of the area and then freezing. When freezing, the expansion of the water could be causing the framing to crack?