I'd start with the charge air cooler. First, start with the boots that attach the cooler to the tubes that lead up to them. That will also cause a fairly noticeable loss of power. Then, I would get the vehicle into a Detroit shop, or your trusted mechanic to do a test for leaks. Make sure you find out if there are any leaks, not just what is "within specs".
You didn't mention whether or not it was a straight truck or a tractor. I'm assuming straight truck.
I would also ask for a cylinder balance test, which, I believe, shows injector function.
Is the crappy mileage a recent thing? All filters recently changed? How about alignment? How long ago? Wheels balanced properly? What brand and model of tires? The rolling resistance on different brands matters greatly.
There's a start. I, along with several others here, listen to Kevin Rutherford's radio show on satellite radio, Trucking Business and Beyond. Midnight on Siruis 147/XM....not sure. Also on weekends from 1600-1900. Kevin is a fanatic about improving fuel economy, and the direct dollars it keeps in your pocket.
Hope I've helped.