I removed the box and installed a flatbed on a Dodge I had at one time. I went "above the wheels" and made the deck completely flat and 9 foot in length. A completely flat deck will obviously have to be higher to clear the tires and your suspension travel... I suppose it depends on what you plan on hauling, how you'll get the load on and off and if you want the deck as low as possible. I used angle iron to extend the rear of the frame and mounted the stock bumper 1 foot back... but if I were to do it over again, I'd just leave the length at 8 foot. I used those round trailer lights mounted on simple steel plates. Obviously, the frame on the truck is not parallel to the ground, so you can either use the existing box "risers" or use them as a template to create new risers. I made my risers out of layers of 2x6... 1/2" threaded rod countersunk through the risers and the frame. I believe I had 4 risers which spanned both frame rails, one at each end and two in the middle. Depending on your gas tank, you may have to either modify or replace the filler tube. My deck was just pressure treated 2x6 with an angle iron frame around the perimeter... I fab'd a headache rack and front wall from steel and steel grating/mesh (that diamond looking mesh stuff). I used eye bolts in many locations on the sides of the deck and the front wall to use for strapping down loads.
Overall, the flat deck worked very well. At the time, I was moving mostly smaller machines and parts... I never did install sides on the rack.
cheers,