Hi
The professionals use a piece of perspex. There are alternatives to expensive silkaflex, we found a very good one at a plumbers merchants. Fill the old screw holes with silicon, cover the hole with a piece of perspex a few inches larger than the old holes. Stick the perspex down with silicon and then run it around the outer edge as well. You could then (belt and braces) use Gaffer (duck) tape as a finale.
Before you do any of that though put a lower cover over the hole, from inside the van and then using either expanding foam or silicon fill the origonal hole.
As Mike says though the leak could well be elsewhere
stew