Remember,
@Blitz is still not 100% sure air is the problem.
I'm still not sure it is ever was an air problem, but I think I found the main culprit.
Things I checked:
Confirmed that there was no air noted in the Racor filter.
I checked all torques (with torque wrench; 20 ft-lbs on larger, 16 ft-lbs on the smaller banjo fittings) to confirm they were tight. Some tightened a little more than previously, so I ran it and had same issues but with no noticeable drips anywhere.
After wrapping the fittings overnight, I did have one small drop of diesel; located at the Banjo fitting at the secondary fuel filter housing from the line that comes from the lift pump. Very small drip, and later confirmed that really was not enough to be causing all these problems. This maybe a candidate for a Dowty Seal type of washer.
I went back to cleaning out the tank again to further look and re-seal the pick-up tube fittings which didn’t appear to have any issues. Checked to confirm air tightness of the pick-up tube as well.
After removing all the fuel (every drop using a small pump type vacuum fluid extractor I normally use for my oil and rags on a stick) I was able to disconnect the tank enough and move it around to be able to get a good look inside the tank to confirm it was bone dry.
I was surprised to find zero debris except for one piece of what appeared to be a fibrous gasketing material that was a little larger than a quarter in the bottom of the tank. I ran a thin wire in the tank to pierce the material and take it out. This piece is a little larger than the original pick-up tube as shown in the photo, and I could image it could easily clog the tube. I have no idea where this is from, maybe it was in there for years.
Afterwards, I reattached all the fittings and put about ten gallons of fuel in the tank. I ran the engine at various speeds under load for over an hour and fifteen minutes with no issues.
I can’t thank everyone enough for your help. Hopefully I'm in the clear now.