Well, this could be caused by many different things but fuel pressure is where I would start.
The DDEC III engines should have a "restricted fitting" mounted at the fuel return line connection. It has a 0.080".(eighty thousandths of an inch) orifice that restricts flow to create system pressure. They do erode so that the hole enlarges and fuel pressure falls off. It is rare but it happens.
So....if you measure the pressure and it is low that is something to check. That is also the place to tap into for doing a "spill back test" if it's suspected that air is entering the system. Aeration of the fuel will definitely effect power.
You should check pressure on the outlet side of the pump and most often it is easiest to install your gauge into the secondary fuel filter adapter.
Ideally you should use a 0-100 psi mechanical gauge and check the pressure at full, no load (2100-2200 rpm). You should see 60 to 70 psi and the gauge needle should not "flutter" or bounce. It should be rock steady.