roof repair help !!

I'm hoping I can get some good ideas here. I have a 1989 Fleetwood Jamboree. 26' long with bunk over cab. Not a flat roof slopes down after bunk. Metal roof.  Was given to me last fall, I sealed where I thought was leaking making a seem separate on ceiling. Well it was neglected too long I openned the seam to see what was there.  Moldy delaminated plywood.  Now I assume if ceiling this way roof is to,right?  Seems ok walking on but can feel the metal is not tight to plywood in area of leak. Can I replace this metal roof with the new white rubber stuff? will the edging on it now hold the rubber?  Watched may you tube videos but have yet to find one going from metal to rubber only rubber to rubber. Had someone tell me "oh just coat it with liquid epdm and reglue up the vinyl you tore to see and you'll be ok."  I don't know about that what is rotten, will a strong wind at 70 mph on interstate make the structure collapse on my kids if too rotten ?    Had someone tell me the metal structurally hold up the bunk and if you remove it it will fall on the cab???? really sheet metal holds up the bunk??? 
Scared to take to local rv place because I took it in for a recall I found on fridge and they fried the control board and claimed "I" must have wired it wrong????  UHH I didnt wire anything  fridge made ice and kept food and beer very cold untill I took it in.  Dometic is sending me a board as I complained to them about their warranty provider.  Been an hvac tech for 25 years and I have made mistakes and will boldly tell the customer "I made a mistake and this repair is free because I made a mistake."  Boss doesnt like it that it is an unproductive call, but he said if I'd lie and he caught me that would be worse. Luckily I can probably count on both hands those kinda oops's in 25 years.
ok enough off topic  what about my roof???
Kurt

I seriously doubt if anything in the roof holds up the bunk or anything else - RVs are very simple structurally.

Odds are the metal on a 1980's RV roof is just laid over wood cross members, but if you can walk on that area then it must have a plywood substrate as well. I think I would open it up and get a better look. Maybe from the bottom. since you know that is bad already.

If you use rubber sheeting (EPDM roofing), you will have to install a plywood substrate and glue the EPDM to that. Edges are sealed with RV lap sealant (usually Dicor brand) and perhaps some molding for trim. I don't see any issue sealing the seam between a metal roof and rubber roof. The material isn't the roblem - it's the amount of movement between the cab-over area and the main roof. No matter what materials and sealants are used, those seams open up from road vibration and twisting. They need regular attention (at least annual).

Thanks Gary,
All I have to do is get the weather to cooperate when I get all the materials. That I'm sure will be the hardest part.