Before you put things back together check the flooring just inside the back of the trailer. That is a very common place for rot because of the way the sheet metal goes in under the floor and conveys water to the bottom of the floor.
Yes that seal under the banana strip is critical to sealing when you are done.
WBCCI 12156 AIR 3144 WACHUNG TAC NJ6
2004 Excursion 4x4
1991 34 ft. Excella +220,000 miles, new laminated flooring, new upholstery, new 3200 lbs axles