Well for starters make sure your truck is calibrated to the right tire size. And double check the speedo with a GPS. Even my Blackmaxx set at 38.5" tires which is what I'm running is out to lunch. I have to put it at 37.00 which puts it perfect within one km/hr. If the computer is registering smaller tires than actual, the odometer is always going to show less miles traveled.
Next pressure test and be sure you have zero boost leaks. I've fixed countless friend's 6.4s who complained about low fuel mileage. Usually multiple small leaks, or a big leak. Holes in boots, loose clamps, holes in the intercooler... Also check up pipes.
One thing I've learned with the 6.4 is small tires or high gearing kills mileage big time. Big tires actually help. Low cruising RPM makes for good mileage since it makes monster torque down low. I hand calculate 17-18MPG regularly. 38.5" rubber, 8" lift, 3.55 rearend, mostly empty. All the first stage mods, on the HD300 tune always. Highway speed 110km/hr puts me at 1500RPM. Pulling my travel trailer @ 9000lb usually gets me about 11-12mpg but never single digits.
Anything over 10k weight I wouldn't try though without re gearing or smaller rubber.