I am no expert, but I don't see a problem with your plan, it's just different from what most folks do; cut down the frame, cut the bed sides, etc. But variety is the spice of life
Have you priced new bed sides and do you have a short bed truck frame? The bed sides are pricey and a short bed truck frame is a mighty popular item.
You'll also need short bed angle strips, short bed center strips and wood for a short bed (if you use long bed wood the holes won't be in the correct locations), not much money though in the overall scheme of things, but not nickle and dime either.