I recently bought a 2006 f150 4x4 5.4L. Didn't get the real story on it. So, here goes. It appears that the truck had been swamped. It also appears the engine was replaced. Very slow cranking. Seems like its off time. Found that the fuse panel was replaced with a 2005, had no power to the injectors. Pin missing. Replaced panel. Ok. No power to #5 coil, pin bent in ECM. Repaired. Pulled lh vc and checked timing marks. Crank at 6:00, right cam at R^12:00 left cam R^ 1:00. Appears that the left cam is my culprit. Tomorrow I'm pulling the front cover and rechecking everything. From what I can find online, I should have crank at 6:00, right cam the R at 11:00 and the left cam the L at 1:00.
Basically, I don't know what has been done to this engine, but it appears someone was messing with it at some point. Feel free to ask me for more info if you think you can help me.