" Large section of my pop top also fluxes up and down in an annoying way at
highway speeds rapping on the overhead bar/lifting mechanism and I'm
wondering if
air getting under the luggage rack is the culprit...."
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I have this problem too, but only when going what is probably too fast for
the stock 2.1L anyway.  At those speeds not only does the pop top rattle,
but the mirrors fold in and wind noise in general is way loud.  My solution
thus far has been just to drive at slower speeds.  However, I had the same
problem with my 76 and decided to address it.  The pop top braket in the 76
is the same basic design as in the vanagon.

I took out the metal bracket (the female portion attached to the van) and
welded in some additional metal in the top of the round hole.  I now have a
mig welder and could do it myself, but at the time a local shop charged me
only $10 dollars.  It was an easy way to make the pop top seal much tighter
and cured the problem.  If I ever get around to a Subi conversion I'll
probably do the same with the vanagon since higher speeds will likely be
more common.
Mike in NC