If I was doing it I would remove it all. Start from scratch put it all back better than before. If you are going to do it then do it right. You will be happier in the long run.
I would first try and figure out where the water came from. Probably window???
Regardless. Remove everything that's in the way... Will be so much easier. Then do the repairs.
You will be much happier after you've finished...
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2015 Sierra 1500 Denali
2014 Coleman 249RB
David Jon Devoucoux
People, Places & Things...for over 40 Years!