You essentially want to create a pick up truck box at the rear for hauling your stuff. Floor, 2 foot walls, and build a tail gate.
Unforchantly, the way the bus is put together will not make this simple, but it is doable. This picture shows how a BlueBird bus is put together.
You will notice that the floor support ribs are not attached to the bottoms of the wall support ribs. Once you cut the roof off at the base of the windows, the sides will be a floppy mess with no structure. To remedy this, you would need to add a formed piece of steel across the top off all the cut wall support ribs. From there the formed pieces would need to be attached to a front for your box, and a rear with a tail gate. Front and rear you would need to build using the same way the bus was built. Rivets and formed pieces of steel. I feel welding is not nearly as strong in this application, nor is it necessary. Also welding tends to cause people to use thicker steel, adding unnecessary weight. Formed pieces of 10 gauge steel are all you would need. It is just a bit thicker than the stock bus floor.
If you leave the stock floor, you need the walls above the floor, and the skirt below the floor to keep it from buckling under load. Also the bus frame flexes without the body keeping it rigid. Without the roof on the cargo area, the bus body will flex and buckle the floor. The bus floor will need to be cut free from the loading box at the rear. Just like a pick up truck.
I'm in favor of flat decks. They are the most versatile, strongest, safest. Need a lift of plywood at home, but don't want to hand load 72 sheets. No problem with a flat deck. Forklift loads, you drive away. Need to pull a 5th wheel trailer, much easier with the flat deck, Something over size to haul, no issue with a flat deck.
I personally don't like pick up truck boxes. They don't force the driver to secure the cargo properly. I cleaned up far too many accidents where all the accumulated junk in the back of some ones truck ended up all over the road.
Newly constructing a flat deck from new steel would be the strongest, safest, and quickest. However, it is also the most expensive.
Hope this helps