Great detective work on finding the leak. Now you can tow in the rain without any worries. You may want to use a product calles Sikaflex on those places. It's the compound thant most manufactures of trailers and even truck bodies use when building or repairing a unit. It has a very thick consistancy that stays slightly pliable for many years, and also works as a glue. You can buy it cheaper at any home improvement store instead of at a RV dealer. Works great for sealing around anything, it's probably what was used around all your roof vents.
Lowell, Amanda, Marley, and Winnie
1996 T-2053 (First Sunline "Little One")
2001 T-295SR (Favorite Sunline)
2003 F-304SR (Last Sunline "The Big One")
1985 T-1650 (Current Sunline)
2004.5 Dodge Ram 3500 5.9 HO Cummins