Chris, I had the same problem on mine way back when I still had the factory fuel filter head on it.
I ended up getting a crappy tank of fuel, so full of garbage that it clogged up not only the New Holland filter I'd switched over to, but the Cat 2 micron downstream of it as well. I posted pics on here at the time of all the black gunk I got out of those filters.
When I tried repriming the system after swapping out the filters, I couldn't get the hand primer pump to do anything. I stoked it until I was blue in the face - some of the crud from the bad fuel had become lodged under the check valve on the outlet of the primer pump, such that it wouldn't seal, and therefore the primer couldn't pull a suction on the fuel tank or develop any pressure in the fuel filter itself.
Not having a vacuum pump, I put a piece of hose over the bleed fitting, and "manually" sucked fuel up into the fuel filter. That's where I learned that #2 diesel tastes just like castor oil.
I managed to get enough fuel up into the filter head, such that working the primer pump again, I managed to flush the crud out of the check valve and the primer pump started working again.
Since you've already "flushed" the fuel filter head, hooking up to the inlet side and supplying fuel from your other vehicle, could be you've already flushed the offending material out of the primer pump and check valve such that it would work normally now.
You can do a quick test - leave the bleed screw shut tight, and just work the primer pump. If it firms up and gets hard after a half-dozen strokes or so, your primer pump is working and you've already cured your problem.
That was inventive, cross-connecting the fuel systems between the two vehicles. You didn't happen to spend some time in the Navy, working in submarine enginerooms did you? Sounds like some of the stuff we had to come up with when underway to keep equipment running and stay out on patrol.
