I read this entire post. From my experience, air is a big problem in the fuel delivery system. I had a fuel filter that was sucking in air and had a ever so slightly leak due to a tiny little tear in that rubber seal. The truck didn't want to start and when it did it took forever and lots of cranking to get it started. However, even with an air leak, it would still run. When I rebuilt the motor in my old truck due to blown head gasket, I used 3 cans of either to get it started and to keep it running. There was lots of air in the system, even after I bled what I could but I had all the lines apart, injectors pulled, everything.
If you do all this work and the truck still doesn't run, don't call it quits. Maybe look for a mechanic who works on farm equipment, good chance they work on old farm equipment and if they do, they will know how the IP works on the deuce. Get a quote to see if they rebuild the entire IP, how much it'll run you. A new pump is $2k or better now days from what I've seen.
Also, when you seat that delivery valve cover bolt, is that little spring in there putting tension on the valve? Did you tighten that bolt 2-3 times over to make sure it is sealing? Otherwise it'll do what mine did, leak and or suck in air. If that bolt has a hairline crack in the mating surface, it'll leak fuel and suck in air. I know you mentioned loosening it and removing it a few times so that's why I asked.
You mentioned you bypassed the fdc and the flame heater, you sure all the lines that were removed, all the plugs are good and tight and if there is a line that is supposed to be re routed back to the IP isn't plugged thus causing the lack of fuel pressure during start up? I've never done it myself but only watched a few YT videos including Tactical Repair when he explained these two modifications.
Sometimes it's amazing how such a stupid simple issue creates a huge issue yet is an easy fix. I hope you get your truck running. I have to follow your post now to see the outcome. I wish the best of luck to you hope to see a video of the beast running!