Did you reuse your flywheel or the new one? sounds like a cam/crank sync. issue but looking at Chry. repair info it should be the same.
Best way to check would be a 2 chan. lab scope to look at them.
Maybe inspect the windows in the flywheel for the crankshaft position sensor, make sure they are not damaged. B
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2003 F-250 4X4 7.3 PSD Crew Cab