Rack complete
Ok so I finally got the rack on. I removed the bed rail caps completely and mounted directly to the bed sides. I used plusnuts, 5 on each side. It seemed that in order to get a solid mount to the bed the plastic rail caps had to be removed. They would become deformed with the weight of the rack and gear, and also be a PITA to line up the holes for the plusnuts. I also put bed liner on the exposed painted surface after removing the bed rail caps.
My rack setup includes: 54" Tracks, Control Towers, 72" Cross Bars, 2 Vipers, 2 Boas, and a Load Warrior.
I plan on cutting down the bars some. I envision catching a tree on one while offroading and causing some serious damage to the whole system.