Try this for #4 option. Buy '54 bedsides without angles and weld angles on a couple inches higher than normal. Leave fender holes in the normal position. The bedsides would sit in the normal position for a '54 but the wood would be 2" higher. Use a '54 rear sill, front panel,'54 splash aprons, 2-1/8" wood blocks and 1-7/8" cross sills so the wood is in the same position as the original '48 bed. Add a spacer between the '54 rear sill and the wood or raise the rear sill 2" higher in the rear stake pockets. Most of the parts needed would be standard parts. It would still look odd when you open the tailgate because the wood would be higher than the tailgate. It might be better than having the whole bed sit 2" too high.
It is usually best if you can use standard parts. There are enough problems assembling a custom truck, without having to do design and dealing with unforseen problems.
Mar-Ktech