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.
There are only a couple spots that will allow air to be pulled in. The banjo at the front of the pump, the mainshaft seal, and the pressure regulator that you changed the seal on just before all this problem started. The pressure regulator compares the pressure inside the pump to pressure of the fuel coming into the pump. Through a passageway that goes to a spot behind the mainshaft seal, which continues on to the pump input, near the banjo bolt. If it is pulling in air at the pressure regulator, you could probably pour/spray some diesel on it and see if it gets sucked in. Or maybe spread some vasoline on it, see if it gets pulled in or anything changes.I think you would have to mess up both of those o-rings to get it to pull in air at the pressure regulator.