I do not believe your dealer can adjust a DMax truck to your tire size - the ABS system yes they could, but for speedo - no.
If you still have the DPF in place, your programmer is causing the truck to regenerate more often and will result in lower mileage.
Your K/N filter is a big no-no for diesels. Yes it may allow more air into system, but more dirt as well. There have been independent tests done that show the stock air filter does the best at stopping dirt.
My truck is an 08 CC/long box and its hovers between 18 - 19 mpg and towing my 28 ft fw and atv trailer in tandem 10 - 12 mpg. I hit the magic 20 mpg mark once in the 38K I have owned the truck.