Personally, I would go ahead and cut a hole in the roof right inside the side doors. Leave the old roof intact for 6' from the back doors. You could then load the boards from inside onto your 6' long shelf. No added doors outside that would need to be secured and/or sealed. The added bonus is the access hole you cut would allow you to stand up inside the van to put on your wetsuit.
When I installed my hightop I left the original roof intact over the front seats and about 36" deep over the back doors. Incredible amount of storage up there.