Could you shift your toolboxes forward? Minimizing the gap between the boxes and the rear of the cab will reduce some air drag. If you can push the boxes as far forward as the front of the bed (or near to it) and put some bulb seal or foam insulation between the front of the toolbox and the rear of the cab it will prevent the air diverting toward the center of the truck when it strikes the leading face of the toolbox as you are having in your present configuration.
Doing this will also open up some room at the rear of the toolboxes that you could use to install some mini-boat tails like the ones used on full-size trailers:
http://www.transtexcomposite.com/pro...ml?ProduitID=3
Some light-gauge metal (aluminum flashing maybe?) or even wood could help reduce the wake area of your tool boxes and bring the effective drag width down to the actual width of the bed at the rear. Installing a sheet of plastic between the boxes from the cab-height ladder bar you plan to install down to a point at (for a long bed) or slightly above (for a short bed) the top of the closed tailgate would be a sort of an aero cap that could easily accommodate the occasional ladder.
I can't recall where I saw it, but I saw pictures of an aero-modded 2nd gen CTD Ram that was lowered and had a pre-COT NASCAR-style custom sheet metal front air dam installed over top of the factory bumper cover. The guy had also installed a GV overdrive and had some pretty high mileage claims, 30mpg IIRC, but it's been years since I've been able to find this. Might have been on TDR (which I don't subscribe to) that someone reposted elsewhere.