Diesel tech claimed the fuel system was full of air and after purging all the lines the motor runs. Question is, how did the air get in there. I have a lift pump at the tank feeding the lift pump on the motor... The tech thought they were causing air to fill the lines due to cavitation.
Just adding to things you could think about. Tech is probably part right, part wrong. "Cavitation" could be just a bad choice of words.
You said you had 16psi, which is good... Maybe too good??? Obviously the gauge will read air the same as fuel. There is always air in the fuel up to the filter/filter housing. Most of it should separate or "settle" out and end up going back to the tank via the return line. If the return line is blocked it could settle faster than it is evacuated. The bubble in the top of the filter housing reaches the top of the pick up tube, starving the injector pump...
I'd find a way to verify the entire delivery path/system, especially the pick up in the tank AND the return line "path". Probably have to improvise something, and probably need to drop the tank. Excess air is as bad as starvation on the inj pump. I'd take it seriously even though it's running now.
You could move the 1st, or put a 2nd FP gauge on the return line somehow... if the pressure is almost as high as the gauge at the inj pump then the return line is probably blocked, or partially blocked. You could also "vent" the return line fitting up front and see if your existing gauge drops substantially, but that wouldn't rule out blockage right at/inside the filter housing itself.
Although there is always some air, it should be a limited amount... random bubbles from sloshing, etc. Using the 2nd/extra pump is a good idea but if the pick up in the tank is partially blocked it will increase the amount of air that gets picked up, the lower the fuel level gets. The extra "vacuum" will "grab" and pass the bubbles through the blockage easier than the fuel. A little blockage at each end would make a good explanation too... Extra air being picked up, especially when the tank is low plus low return flow... it might have taken both to start to "accumulate".
The more I think about it, blockage at the pick up is probably the first thing (ideally) that I'd check... but since it means dropping the tank, I'd take the extra time to check the return path while I was at it. Initially, I was trying to think of something to check before dropping the tank.