Sounds like you might have some air in the system. Is there a primer on your fuel transfer pump? The transfer pump should be on the driver's side of the engine, just below the fuel filters. The fuel line going from the filters to the inline pump should have a banjo fitting that has a 10mm bleeder screw in it. Loosen that and try and prime the fuel system by hand. There should be another bleeder, on top of the fuel filter housing on the return side that takes a 12mm wrench. You might loosen that one and try and get fuel out of it too. Try and keep pumping until you get fuel with no air bubbles in it and the primer gets hard. If that doesn't start it. Crack the nuts on the fuel lines that go into the injectors and crank the engine until you see fuel squirting out of them and then tighten them back up. It might be something else yet but should be a good place to start.
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'04 F550XL reg. cab. ZF-6 speed. EGR delete. Coolant filter. Cat EC-1 coolant. LF777 bypass oil filter. Blue-spring fuel pressure regulator. ScanGauge II. Glowshift fuel pressure gauge.