RV Repair: Pop-up Roof Repair, fleetwood dealer, aluminum skin

Question
Please help!  I bought a used Coleman/Fleetwood Taos recently.  Apparently, the roof had been leaking for some time around the air conditioning unit and has caused damage, both inside and out, around the A/C hole.  The roof on the camper appears to be made of aluminum, Styrofoam, wood and vinyl – in that order.  I would love to be able to replace the roof or take it to my local dealer, but the fact is I simply don't have the money.  However, I am relatively handy and have plenty of time to work on repairing the problem if I just had some direction on what I need to do.  I am especially concerned about the appropriate materials (adhesives, screws, rivots, tape, etc.) to use when working with the various layers of the roof.  I am also concerned about maintaining the structural integrity so that the roof will support the A/C without damaging the roof further.
Unfortunately, I am not an engineer so I am unable to determine what holds this whole thing together.  I'm surprised that it would hold up an A/C even without damage!  I was hoping you might be able to provide information on how to proceed with repairs.  
The inside damage is confined to an area from about the middle of the A/C hole back to the rear inside roof support, and about 18” to one side of the A/C hole.  In the area the wood layer is clearly rotted, but hidden by the vinyl.  I'm not sure about the condition of the foam on the inside side.  The outside damage is limited to the aluminum skin pealing away from the foam and A/C support braces (aluminum) over a small area next to the A/C hole about 10' by 12”.  I went to my Fleetwood dealer who sold me some caulk that was supposed to seal the aluminum to the foam, but it didn't stick.
I would like to replace the rotted wood on the inside, and correctly seal the outside.  I would also like to add additional support around the hole, if possible, before I replace the A/C.  Can you help by providing information on the best way to tackle this problem?  

Answer
A few questions first.

1.Is the wood in panels like paneling or slats?
2.How thick is the foam?
3.is there any aluminum framing at all on the underside of the roof?

I havent found any caulk that works when sealing aluminum to foam blocks, I have always used an epoxy safe to foam. You can get almost any kind of epoxy at Home Depot or Lowes, just remember to test it on your application before using it. The best way to repair the roof top on popups is using aluminum sheeting and rivets then adding a rubber sealant of some kind such as Kool Seal or Rubber Roof. This will help with structuaral support and leakage.