I like to keeps things simple, start with the air intake - a Diesel is an air pump, loves air more than fuel, keep that in mind when looking things over. Diesels hate water in their fuel. I have found if the E.G.R is all coked up, things don't run right, it acts like the Diesel is suffocating, can´t breathe properly. Easy to clean if you can get to it. Be careful with age comes brittle. Also check compression - there are Diesel compression testers. Have your oil annualized, chevron corp will look at your oil and break down what is happening inside the engine.
I should have asked this first, are you running bio fuel or Diesel fuel? or do you switch it up? Just remember that bio fuel will clean everything so fuel filters will get blocked up, fuel pumps go bad, any rubber in the fuel system will go bad O rings and such, have to switch to polyurethane.
Hope this helps, I work on buses every day Diesel and electrical.