Ahh, as I was reading down the list of symptoms I thought, there's air in the lines, which means his overall pressure at the injection site is crap. Lots of air or even a little air makes the diesel lose its hydraulic pressure. So instead of getting 155 bars at the injector, you might get 100. OR less.
So yes chase the air from the crush washers on the fuel filter to the IP first. Get new ones or look really hard at the ones you have first and see if they have scratches on them that would be letting in air. Now, I have taken them off, heated them with a propane torch to reaneal them and put them back on with success.
If that doesn't solve the problem then you have to look at maybe that top seal or the throttle bushing as a potential source of the air. Like you say a real pain to have no visible leak but yet air in the system. It is due to the fact that a vacuum will put air in more than pressure will push it out. The vacuum on the system is from the front side of the IP.
You might also try running it off a jug on the front end just to see if that clears up the problem. If so you need to look at that filter to tank area for a source.
That's my take. Glad mine purrs like a kitten and now with the new air shocks in the back I won't be slamming every pothole in town. And there are a bunch of them.
I had a thought about this last night. In theory, if I block off the fuel inlet and the injector return, I should be able to put my vacuum tester on the outlet, and if all the seals are doing their thing, I should be able to build a bit of vacuum on it. If not I think I should be able to spray a bit of diesel on points where there are seals and see if it get sucks in.
Fuel going into the pump is perfect; no bubbles that I can see heading into the pump through my clear lines; I only get bubbles on the outlet when it is running, and when I shut it off, they do roll back to the pump, but not like when the front seal was leaking. They just mosey up to the pump over night.
Curious, if the pump is perfectly sealed, are air bubbles on the outlet line still ok? Or should it be a perfect line of fuel? I would suspect you would get some bubbling just due to the return lines from the injectors.