If the area under the tool box is badly rusted, then the floor is badly rusted. Why? the floor IS the bottom of the box. I'm sorry but the only way to do it right is to remove the tool box and replace the floor pan with a quality pan, then replace the box. If you destroy the box while removing it there are after market boxes available.
Sorry there are no real short cuts here. If you have metal skills it really isn't that difficult. Some will argue with this, but the floor pans were glued in with automotive quality glue right from the factory. So, all you might need is an angle grinder with a few cut off wheels.
