Ladder rack with tunneau cover? (Undercover Flex)

I have an undercover flex (triple flip top) hard bed cover for my 2013 long bed. I've had this cover for a couple years now and really like it. However, I've run into a problem in that I want to be able to haul 10 to 12 foot Paddleboards with the cover intact so I can store my gear (dry). The problem is that there are no overhead ladder type racks that I can find that will work with this particular cover. The only options I could find:
1) Replace the cover with a Bak flip dual cover/rack dual system. Looks like a good system. However, I've got over $800 in my current rack and the replacement system is $~1600. Uggh!
2) Install low profile hauling bars (like Yakima) on top of the bed rails. Problem with this is I'll have 6ft of boards hanging off the back of the truck. And again, I would have to take the bars off to access gear under the cover. I really need these boards to be overtop/overlapping the cab and would like to be able to access my gear.
3) Setup my hitch canoe carrier in long pole mode and install a single rack on top of the cab. This will limit how many boards I can safely carry and spans the load a little bit further than I’d like to. Stability wise it’s a little wonky.

The main problem I’ve found in my search is that there are “sport type” racks (this is not a work truck so I don’t want to install your typical work truck ladder rack that comes over top of the cab) that I can make work by mounting to the top of the bed rails. However, I won't be able to flip the cover because the uprights of these rack systems are angled in toward the bed for aerodynamics, ergo (look), and strength. So essentially, the flip top will hit the rail uprights when trying to flip the cover up so they won’t work together.

Anyone have this particular cover and need and found a workaround? Or anyone have a creative idea? Thanks all!

 

I ordered a contractors rack and can't find any information about tonneau covers that can be modded to work. I've ordered this rack http://www.ebay.com/itm/Paramount-1...-Truck-Contractors-Rack-/311300880733?vxp=mtr