The more I think about this, the better my ideas get! ;-).

Replace the whole rack with a custom designed high top storage box!

Take off your rack, and have the fabricators make a mold of its base,
and then form a high top unit built on top of the base you just molded.
This way you will have a one piece unit with more storage capacity that
will fit perfectly on the roof yet could still be removed if desired.
Just attach it the same way the rack is attached, but completely sealed
around the bottom.

You might check with Ed Anderson at Adventure Wagon in Fort Bragg
California if he is still around.  Last I heard the molds for the
Vanagon were for sale, and that would save you lots of money and time.
You would only have to fabricate the back of the box, and you could use
your rack for the lower part of that mold.

Stuart, at home relaxing now with a glass of wine.