On a Dmax, almost everything is based off of fuel supply! Boost is directly related to fueling, Allison shifts based off of fuel quantities "torque".... There is no external lift pump to supply the CP3, so the CP3 has to pull fuel from the tank, thru the filter housing before it even gets to the CP3 to get pressurized. The ECM is going to make all the adjustments it can to keep the truck running down the road, with the fuel the CP3 is able to pull out of the tank, eventually it throw a code and you will not be able to accelerate over 1800 rpm, if there is a restriction. IE: Demand more rail pressure to compensate for the lack of fuel; the Injection process it what gives a diesel its "tick", so more rail pressure means louder "tick".
Change the fuel filter! Its a $45 fix that is not wasted, and if it fixes it, it would have saved you alot of work. If it doesnt then you can start wondering what the deal is.
No seriously, change the dang filter...
Caleb