For cleaning the injectors I like to use 1 gallon of diesel, i bottle of GM upper engine cleaner, and get 2 sections of hose about 3 feet long(1/2" and 3/8"). Mix the bottle of cleaner in with the diesel, disconnect the fuel lines at the rear drivers side of the engine, hook up the 2 pieces of hose, run them into the can of cleaner/diesel mix, then run the truck for 20 minutes, then shut it off for 20 minutes. Repeat this process until the mix is gone. The GM cleaner is REALLY good stuff, and when you shut it off, it gives it time to soak i nand break deposits loose, then you start it back up and it flushes the gunk out. As to your tuners, diesel day dreams has a good rep from what I could find, but couldn't find any info on the other place(not always a bad thing). I will say most tow tunes are not good for milage as tow tunes normally keep you on boost to help with throttle response, limit smoke output, and keep EGT's down. True economy tunes will lower boost, raise the timing through the roof, and probably bump some rail pressure into it. All of which are bad for tow tunes. As to trans shifts, I personnaly like to leave them alone on the 6 speeds for the most part. The 6 speeds already have pretty good shift points to them IMO, and I see no real reason to alter them for most. And since you say you have a dually, it's never going to get great milage. Also are you hand calculating your milage or going off the lie o meter. The factory DIC is KNOWN to be WAY off on some trucks, hence why most call it the lie o meter.
And anytime you have fluctuating balance rates like this, it is normally a good idea to also do a compression check on the engine. Since you're not the origanal owner, you have no idea what was done to it before you. it is most likely injectors, or high fuel temps causing your issues, but a compression test is good peace of mind. For your truck, I would reccomend a good DSP2 tune with an economy tune for running empty, and then an optimized towing tune. And while I'm thinking about it, how are you checking balance rates? Your milage does sound a bit low to me, but not out of the realm for a dually. I know I have my tunes running around in several single rear wheeled trucks getting an honest 21MPG on interstate at 70-75, and one in a DURABURB getting some pretty good numbers hauling his camper across country towing. How did the milage compare when it was stock to tuned?