Most of the MFR manuals have a good troubleshooting section for their engines based on stack emissions.
But you want to run through the fuel system, injectors, pumps, rack setting, take cylinder pressures to see if you have an abnormals readings, ect.
On the air side what is the turbo putting out, what is going through the intercooler-set up a u-tube manometer, what is the turbo readings compare on history and so on.
Oh and check for bootleg injectors. They may have snuck into the ship stores.
Here is a list of some causes:
Dirty or worn injectors
Faulty turbocharger (ie not enough air to match the fuel)
Incorrect valve clearanceIncorrect air/fuel ratio
Low cylinder compression (eg sticking piston rings or worn components)
Dirty air cleaner
Restricted induction system (eg system too small or kinked inlet piping)
Other engine tune factors including valve adjustments, and regular servicing of air, fuel and oil filters. Do not buy fuel from suspect outlets.
Poor quality fuel
Excessive carbon build up in combustion and exhaust spaces
Cool operating temperatures