The door beam/duct isn't the problem, it's where the mice are getting
in.  

In a GL, there are only two places where mice can get in (besides
windows left open).  One is the front fresh air intake behind the upper
part of the grill.  A good solution here is to cut 1/4" galvanized wire
mesh to fit over the opening.  Install behind the secondary plastic
grill that comes factory.  This will keep mice out of the entire fresh
air system.  Be sure to cut the mesh a little large to bend around the
edges, the plastic grill there doesn't actually touch the body metal and
that's where they get in.  Assuming the bellows at the door hinge are in
place.

The second location is the fresh air exits in the rear of the later
models, the plastic things at the rear edge of the rear side windows. 
On my van mice had chewed the foam away, as well as perhaps some of the
anti-draft flaps.  To fix this I used 1/8 galvanized mesh cut into ~1"
strips and screwed to the rear opening in the side vent grills.

Unless you're missing a grommet or door seal somewhere, this should keep
the varmints out!

I once had a mouse die in the bottom of the c pillar, the rear side of
the front door opening.  It was an awful smell that took a long time to
find.  When I did find it (with the help of a mirror) I used a flexible
grabby tool to pull out the dead mouse, and also had to remove the plug
at the bottom where the early a/c drains left.  It took some cleaning
let me tell you.  Enzymatic odor eliminator product worked well.

Gregory Smith
'88 Vanagon GL

Smith Design Studio
Small Building Company
Olympia, WA
360-239-0429
gregoryfsmith.com