Roof seam repairs

Hi there,

  I just started working on my '76 Prowler, and I'm investigating and doing demo work on the roof.  I'm looking for advnice on how to proceed with roof repairs....

At the back of the roof, there is a weirdly folded and screwed seam between two sheets of aluminum that seems to be the source of water damage.  The top sheet folds up and back over itself for about an inch, the bottom just extends under the top, and they were screwed together, no washers, with butyl in between and a lot of silver putty covering the whole shebang.  The top sheet fold scoops "up river" if you will, so that dirt and water get caught in this pocket.  The screws were definitely not waterproofed other than being covered by putty.  I have removed as much of the putty and all the screws, to have the two sheets un-coupled.  I'm wondering if I should replace a whole section of the aluminum, and maybe move the seam a few inches down, so that it's right above the tail lights, rather than on the horizontal part of the roof.  

There's also a section above the kitchen that has slumped, and has been coated with a black tar kind of material, then over coated with roof rubber.  Is there a way to fix this without replacing that sheet, or the whole dang roof?

Thanks!  Photos and videos of what I'm talking about below...

The seam before I took the screws off
Prowler roof explorations by Kate Clarke, on Flickr


Here's a video of the un-screwed and loose overlap
IMG_5551 by Kate Clarke, on Flickr

exposed seam and tank vent
IMG_5531 by Kate Clarke, on Flickr

Detail of the seam at the edge of the roof
Prowler roof explorations by Kate Clarke, on Flickr

tarred and slumped area of the roof, over the kitchen area.
Prowler roof explorations by Kate Clarke, on Flickr