Determine what deck height you would like. That will help determine if you just put a wear strip between your truck main frame and your flat deck subframe or rip a timber (width of truck frame) to accommodate your finished height.
This is what I was used to doing as we did all loading dock work.
Regarding stake pockets. I would get someone with an iron worker to bend up "C" brackets to accommodate 2x4 or whatever size stakes you plan on using. "Wrap" /weld the pockets with matching width flat bar (horizontally) the length of your deck as a "rub rail". This will give your outer edges of the truck body a finished look as well as providing chain down and tie down areas.
Terry