I am on my third design of my bed, and have been happy enough with this one to have left it alone for almost three years.
Things I learned:
-Make it easily removable, I have only three components: sleep shelf, supports, and cargo box
-Cargo Box: Make it as big as you can between the wheel wells, the only real wasted space is in the back corners. Also build the cargo box with a high back and sides in the back so nothing can come out. I added the separators to hold my sand bags in place and also limit things sliding around. Combo of the plywood, 6x9's, and 2x4's
-Sleep shelf: Somewhere I saw a hinged side that makes it easy to remove and allows me access to gear stored there even when in the truck. I put the shelf as low as possible pretty much right on the wheel wells to give myself the most sleep space and most height once in the truck. Definitely at least carpet, I did double carpet padding but did not know about paco pads then, but more than anything to cover the wood for slivers. Pretty sure I used 3/4" plywood. I am sure you could just split it down the middle and have two sections without the hinges
-Rails: Just three 2x4's support me and the dog fine, and I am a big guy. I have a duraliner in my bed and it has spots for the wood to fit in like many people before me have done this, which worked out awesome. Sure you can rig something depending on liner or bed that will work.
Its snowing so pics are little shady, and my camera is about to die