You have fuel "filters" as more than the factory one?
If so, the factory pump may not be able to keep up. There are some threads on about the demands, filters setups, volume checks post filter - could be your issue.
Another thing to look at is how much fuel is actually getting to the pump (franklin2's post). If I'm not mistaken there are some problems with the fuel p/u tubes in the trucks. They fail and your not able to draw enough fuel when moving (sloshing around). Also the p/u screen or opening can be block by debris (dirty fuel or rust in tanks).
When I had an issue like this with the old gas engines, I would disconnect the line after the pump and check for flow by having someone crank the engine (disable) while I held a container - like a two liter bottle and check flow.
On these engines, you would need to deactivate the injection pump just in case you have enough fuel to spin the motor around a couple of times.
Once again, search the previous post on the subject. Sorry, just not much help in the procedures.
If your getting air into the system, fuel would most likely be getting out. You would smell diesel and/or see diesel puddles. I know I did when my return o rings were starting to fail.
Don't rule out a bad pump (incorrect size on the diaphragm - no leaks, couldn't draw enough fuel, it happen to me once on a gas engine) or a collapsing rubber line either. I'm not familiar with the fuel line set up from the tanks to the pump on the trucks. But you could have a collapsing hose.