I own a 2008 Ford F350 dually with the 6.4l diesel engine.?

When we first saw the vehicle at the dealer it had just been traded in on a new truck and the Sales guy said the truck needed an injector and after the tech installed it we were able to test drive the truck over a weekend. The truck had good power and was getting about fifteen mpg. The only thing that seemed odd to us was the fact that the "cleaning exhaust filter" notice came on a lot. We were ured this was normal by the sales guy. Jump forward...bought the truck for towing our travel trailer and boat and the first trip out was just towing the travel trailer for hunting season. We took off from the house and were happy with the pulling power of the truck. After about seventy miles though the cleaning exhaust filter notice came on and wouldn't shut off, then the truck started losing power and felt almost like it lacked turbo, but I could see the boost and hear the turbo working so it had to be something else. A few days later we were able to get it back home and into the shop and they said the left side wiring harness for the injectors was bad and they replaced it. Same side that had the bad injector before. Got the truck back and power is back and have pulled the trailer a couple of times without any loss of power, now however instead of getting fifteen mpg we are only getting about 10 mpg empty worse if loaded. Any clue to why we suddenly lost 1/3 of our mileage? We took truck to a different dealer and the said there were no codes. Could it be a clogged exhaust filter from running with the bad injector and then the bad wiring harness? Any help would be greatly appreciated. We live in Colorado at 6,000 feet above sea level and use diesel additive with cetane booster with every fill up.