It's so sad to see this forum neglected all winter long. For that reason I decided to modify my Cape Horn 15 today and post the pics.
I picked up a spare day hatch cover from the shop where I bought my kayak. I then attached a Scotty fly rod holder to the second hatch cover so I could switch off according to my objectives. Also, I figured if I ever wanted to sell my yak, the prospective buyer might not want a fly rod holder attached to his day hatch. Hence, two different hatches.
I wouldn't troll with this configuration for fear that a large fish might dislodge the entire day hatch housing. I'm positive it wouldn't rip the rod holder off the hatch(four stainless nuts/bolts + a fair amount of Gorilla Glue for water tight seal). When I troll I'll probably attach the rod to my PFD for easy access. This kayak setup is more for transportation to different spots while the rod is rigged and ready to go. It sits right behind the cockpit on the right hand side.