Check the sediment bowl, Im going to take a guess that it is plugged. You can also check the elbow that goes into the bottom of the fuel filter housing, it is a one way check valve, but I have seen it get plugged as well.
I could see a bad diaphram in the charge pump introducing air into the system.
I have had all the fuel lines off our 4430, and flushed the main tank and the whole system. We had an issue a few years back with someone putting dirt and I think sugar into our belly tank of the tractor which caused all sorts of problems. When I got it all cleaned, and put back together, I couldn't get the air out of the system. Turns out there was air in the injection pump and wow it was a headache to get out. Cranking injector lines is what allowed me to get it out, but in the end, I had to be on the ground bleeding, and pumping manual primer, while having someone in the cab starting it.
Also remember there is a shut off at he bottom of the front tank, in the hole in front of the front axle. Shutting it off makes life much easier to clean bowl, etc.