I finally got this thing drivable again and took it to my local welding shop for some stainless welding.
The "bunk" is now connected to the stainless radius panels on the front of the box. The bunk area is now water tight.
Now comes the fun parts. We ripped out all of the old oak flooring, and replaced the I beams that were over the rear tires. They were rusted beyond belief from the road spray. The current plan is 3/4 pt plywood with 3/8 hardee board and porcelain tile. I ordered some mobile home under lament to go between the plywood and the I beams. That should keep the water out nicely.