Thoughts and/or comments:
1) do you have the 1s gen OEM filter head (drivers side fuel heater plug smaller than the other plug) or the 2n gen OEM filer head (both plugs about same size and heater plug likely bright blue). If you have the former check for a massive air leak by unplugging the heater plug.
2) is the WIF sensor at the bottom of the filter on tight?
3) I gather both old filter "O" rings are off and both new "O" rings are on, correct, and that you ran the filter down until the gaskets/"O" rings bottomed and then did about 1/2 to 3/4 more of a turn, correct?
4) the filter bleeds just like brakes - pump until you get pressure; hold pump down and open bleeder (I like to run a clear vinyl tube to a catch bottle so I can see what's happening and keep the mess down) to release air/diesel; tighten bleeder and release pump; repeat until air is gone. If you leave the bleeder open during the operation I strongly doubt you will ever do anything but pump air in and out of the filter head.
5) if you removed the assembly from the vehicle to swap the filter (easiest way to do it) did you reverse the fuel lines on reinstall?
6) I suppose it's possible the fuel filter pickup screen in the tank is clogged but you would have to drop the tank to check that. Just a thought, if you lack an inline pump - remove fuel tank cap, use a tennis ball to plug the opening, open bleeder valve or remove feed line from filter head, LIGHTLY pressurize the fuel tank by inserting an air supply line thru the tennis ball which should force fuel out of the tank and on to the filter head unless the line is plugged somewhere between the tank and the filter head.

Well I had success with filling up the bleeder port, the jeep now runs. The plunger still doesn't build resistance, so something must be broken. Thanks for the replies and troubleshooting ideas. Guess I'll eventually have to get the 2nd generation filter head.