Aluminum Roof Repair

[Phlamber]

So, we have a 1978 Fleetwood Pace Arrow with an Aluminum roof.
This thing has seen better days and we're doing what we can for it.
Currently we are fixing the roof.
We have removed most of the old roof coating using Jasco paint stripper (wonderful stuff!) with a paint scraper and sandpaper. It looks as though someone used Bondo(?) in the past to make the roof flatter.
The leaks have caused the thin layer of wood that sits between the roof and the styrofoam insulation in the ceiling to all but rot away. As well the steel beams that support the roof and ceiling are rather rusty.
Now, when this thing was put together they didn't leave much overlap on the sides of the roof. So, whatever​we do to it we have to keep that in mind.
The roof is dented in many spots. In fact, it says down severely right around the front vent/skylight before sloping upwards again sharply to where the vent actually sits/attaches.
I personally think that we should unscrew the sides of the roof and remove the old rotted wood and replace it with 1/8" plexiglass, or something similar. My boyfriend thinks that we should use something like Bondo and just flatten the outside of the roof.
All this would precede us painting the new elastomeric layer on, of course.
We don't have much money. But, we both recognize that spending the right amount of time and money now could save us a great deal of money and hassle later on down the road.
(I will post pictures of the roof as soon as I can get decent lighting to do so in.)