Here's the scoop from Dave Fritz's site. Step 12 covers bleeding air from the lines which is probably where you're at now. Good luck!
Step 1: Drain the filter using the valve.
Prop a 1 quart oil bottle on top of the front diff to catch fuel from the drain tube.
Open the drain and immediately loosen the housing nut enough to loosen the housing. The fuel will siphon if you don't "break the seal". After that just let it hang there for a minute until the housing empties.
Step 2: Disconnect the water sensor connector.
Using a long screwdriver, gently/slightly raise the end of the retaining clip and slide it off.
Step 3: Loosen canister retaining nut on header while holding canister.
The filter may stick to the top bracket and dribble fuel all over everything if it is not popped free from the bracket before removing the canister.
Step 4: Twist and remove old filter cartridge from canister
Step 5: Clean the canister and wipe the gasket surface on the bracket.
Step 6: Lubricate gasket and O-ring and then install on new filter cartridge.
Step 7: "Replace center O-ring with new one provided.
Step 8: Install new filter cartridge in canister.
Step 9: Pre-Fill the canister with fuel.
Some skip this and fill later by removing both plugs from the top and filling through one of the open ports.
Step 10: Install canister on header with drain aligned as shown, and tighten retaining nut to 10 ft-lbs.
Step 11: Reconnect water sensor electrical connector.
Step 12: Prime fuel system.
Loosen the test port fitting towards the front of the engine (closest to the center) on the top of the housing. This is the "outlet" test port.
"Bump" the starter without letting the engine start. The electrical fuel pump will run for about 20 seconds. Give the pump a few cycles before proceding. Watch for fuel at the loose plug-tighten.
Some pull the injection pump relay to run the fuel pump without starting the engine, but the FSM warns that a fault code may result and require the DRB to re-set it.
Step 13: Start engine and check for leaks. Correct as needed with engine off.
The engine may not start, or it may start but die. If it does not start and run, bleeding the fuel lines may be necessary. Begin at the filter and contine along the fuel line to the injector pump until all air is purged. Torque the banjo bolt to 18 ft-lbs.