Several months back I was faced with the same dilemna, how to carry a
canoe on Vanagon equipped with a pop-top.  I'm perhaps a bit more
sensitive to rough roads and extreme conditions than most (it is currently
-49 degrees F. outside - but then it's on toward midday and that's a
warming trend).  I was uncomfortable with mounting anything to the pop top
and already had racks equipped to handle 6 bikes (one a tandem), a buggy,
two tents, helmet bag, etc.  All this was set up to allow opening the
top without removing any bikes or assorted paraphernalia.  So I researched
what was available and decided the best setup for uprights was orignially
made by Thule.  Unforthunately, Thule had discontinued those racks several
years ago and I was unable to locate any.  So I received a set of drawings
from Thule for the uprights, fabricated a set and modified them to
accomodate Yakima bars.  Total investment was less than $10.00 for the
Yakima parts and scrap 4130 tubing and sheet metal for the rest.  

Now I can carry a canoe along with the bikes with nothing touching the
vehicle or the top.  email if you want more info.

Fred