At the recommendation of my yard, Sintes Boat Works, I used black Silaflex on the inside and white on the outside. The black helped make a consistant blend with the dark tint while the white matched the external paint. The job cost about $100 total including glass and caulk. After 1.5 years - no leaks!
Reference:
http://www.silaflex.com/Here is a photo of the back window. I'll try to find a better shot.
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