roof seals failing

I've started the mammoth task if stripping the old carpet lining and rewiring. Unfortunately I've found huge rust patches in both rear corners and it looks like the seals where the fibreglass she'll meets the body is failing and that's where water is getting in. How can I clear, treat and reseal the rust to make it watertight? Where they originally cut the roof off they've just bent the sides over and screwed into a bit of wood then into the fibreglass shell. 

Also can anyone recommend the best way to get rid of the old adhesive and fibres thats left after stripping the old lining off? Cheers all :)