This is a big deal and VERY common to Class C's. I have a 2003 Itasca and have a similar problem. I have tried searching the web for solutions. I will share some of the links I have found. I am collecting info while I formulate my battle plan. I hope to fix my water damage myself, in the meantime my leak is stopped with RTV silicone. If anybody has more links, please share.
http://www.ecalypso.com/
http://www.class-c-motorhome-info-made-simple.com/water_damage.html
http://www.irv2.com/forums/f87/bunk-water-damage-rebuild-93178.html
http://www.irv2.com/forums/f87/class-c-cabover-water-damage-132583.html
http://www.delamrepair.com/composet_2_002.htm
https://plus.google.com/photos/100179824430630761844/albums/5773296653657380769?banner=pwa
My damage is not as bad as the damage above, but it is not going to get any better. It is not going to fix itself. That pesky horizontal seam on the lower edge of the cab-over is the culprit. It is a design and manufacture defect common to a lot of Class-C's.
The fix? What I believe is that the whole floor of the cab-over needs to be replaced. While that is off, I will inject resin in the side wall of the cab-over and re-laminate the plywood and fiberglass skin. Since you do not have flat fiberglass side walls, damage there is hard to see, but expect it.
Good luck to you.
RVMike1