If changing the filters helped for a while it is pretty much definitely a fuel supply issue. You almost have to have crud in the tank that is stopping up the filters. Otherwise changing the filters should not have provided a temporary fix. Most of the medium duty trucks like that have aluminum fuel tanks with drain plugs in the bottom. I would start by totally draining the fuel tank and flushing it with clean fuel. Then back flow the fuel lines with air pressure. Install new filters and put new fuel in the tank and test drive. If it still is not right then you need to see what the fuel pressure is at the common rail. Its possible that the CP3 has been damaged by lack of lubrication.