Very good ideas so far. I can't stress enough the incentive plan. I can tell you from firsthand experience that people drive much differently when they're not footing the fuel bill (or in your case, getting a bonus for NOT using a lot of fuel.)
I think a hybrid system would be ideal for these trucks, as they waste fuel spinning up the turbocharger heading uphill, and then waste the momentum with the Jake brake downhill. Running the engine to keep up the electrical, air and A/C while parked is another problem easily solved by such a system.
The problem, of course, is the weight of the batteries. With a mandated 80,000 pound limit, every pound up front is a pound that can't be carried (for profit) on the back. Maybe the NTSB can come up with rules that allow the extra weight of hybrid systems to exceed the 80,000 threshold (say, 80,000 max allowed, plus up to 2,500 pounds of batteries.)
As to your problem, is there any way to enclose what's loaded on the flatbed? Maybe a curtain-side trailer with a boattail on the back, like
these?
Tim