oops, didnt finish last message, trigger happy with the mouse...
the way to fix is to stop the water getting in and thoroughly dry the insulation.
then you need to clean throughly and apply some aluminium etch primer on the inside surface of the metal, followed by some paint - i used smoothrite. this will coat the metal inside the van to prevent the oxidation from continuing by cutting off its supply of oxygen.
on the outside, run down and prime holes as above and fill with automotive filler. paint affected roof to match rest of van.
its a lot of work depending on how big the area is to be done.
another alternative (assuming the roof is flat alumininum rather than dimpled) is to cover the whole section with a fresh sheet of metal, and repaint to match.
hope this helps - good luck.