I had a similar problem. If I did it correctly you can look at the pics of my repair (there should be an easier way to post pics...this is an pain). I used a razor knife and cut out the rotted wood (really just luan plywood) dried it out using a heat gun, careful not to overheat. Then I replaced to foam covered it with a pices of gelcoated piece I got at Micheal's craft store and pop riveted in two pieces of aluminum strips to hold the new piece in place and glued down the velcro strip. I did the repair before I stored the camper for the season. I also re-caulked the door and tighten up the clamps the seal the door. I plan to replace the seals this year. I find out if it leaked when I pull it out of storage in June.
http://i103.photobucket.com/albums/m140/JimChow/PICT0169_zps2204871d.jpg
http://i103.photobucket.com/albums/m140/JimChow/PICT0170_zps911cce51.jpg
http://i103.photobucket.com/albums/m140/JimChow/PICT0171_zpsdcb37051.jpg
http://i103.photobucket.com/albums/m140/JimChow/PICT0174_zps41607524.jpg
http://i103.photobucket.com/albums/m140/JimChow/PICT0177_zpsc3707133.jpg
http://i103.photobucket.com/albums/m140/JimChow/PICT0184_zps0fd5cd7a.jpg
http://i103.photobucket.com/albums/m140/JimChow/PICT0186_zpse4463212.jpg
http://i103.photobucket.com/albums/m140/JimChow/PICT0188_zps9329d19a.jpg
Jim & Kathy
Bailey, waiting at the Rainbow Bridge
Gracie, a rescued 6 year old Beagle
2007 Chevy Tahoe
2008 FR Surveyor 233T