I don't think I stated that I started out by cracking all the hard lines to see if there was a change in the misfire or sound and there wasn't. I then replaced the injectors which didn't fix the problem.
When I stated that I "bled the fuel pump", I did exactly that, I loosed both bleeder screws on the top of the fuel pump and bled the air out of the pump then continued bleeding the system down the fuel lines to the injectors.
When I stated that fuel wasn't reaching the third port on the fuel pump, this occurred while I was rotating the engine to check the fuel injection timing. It had nothing to do with the fuel system purge or primer use.
I removed the entire fuel system except for the fuel pump. I cleaned everything and reassembled it.
I partially disassembled the fuel pump and removed the plungers. I inspected and cleaned them all including the piston function at the bottom of the pump, they work fine. While there was no visible dirt, or contaminates, I still sprayed everything with carb clearer.
The one thing I did notice was that the poppet under the problem port seemed to stick for some reason. This appeared to be due to how it was machined and not debris or contaminates. I would clean it then poke it with a clean plastic spray can straw and it wouldn't open. Then it would drop out and I'd put it back in and it work freely again. Then stick again. I inspected it for burrs and saw nothing, nor could I detect any from running my finger over it. The orifice it was seated in seemed very smooth. I hit the poppet with some 400 grit sandpaper, cleaned and replaced it.
I started the engine and it still knocked. I gave the third port a couple light whacks with a small hammer for good measure and still nothing (thought it might free the poppet). I was checking the fuel system for air bubbles bleeding everything while the engine ran then suddenly the engine knocked like **** and died.
From all the fuel system purging, I had run it out of diesel. I added some diesel, purged and restarted the engine. It started and ran without knocking. It did continue to smoke for a time then the smoke stopped. I ran if for an hour and the engine now runs better than it ever has.
What it was is anyone's guess but it sure wasn't dirty fuel. I bled and flushed two gallons of very clean diesel through the system.
Problem solved.
Thanks for all the help and suggestions.