I am completely stumped here. I just bought a 2006 F150 with the 5.4l 3 valve triton engine about 5 months ago with 85K mi on it. Now at 90K the truck out of the blue starts to idle rough and shortly after the check engine light begins flashing. Pulled into Autozone and scanned P0300, P0301, P0305. Misfires cylinders 1 & 5.

Here is what I have checked so far:

-Spark Plugs (replaced ALL - what a pain in the ***)
-Coils (swapped & reapplied die-electric gel, problem did not follow coil)
-Fuel Injectors (swapped, problem did not follow injector)
-Cam Sensor
-Compression Check (engine has good compression)
-VCT Solenoids (replaced, problem seem to very slightly improved but still idling rough)

I'm about ready to throw in the white flag on this and take it in to the dealership - which I fear I will be told it's major $$$$ even if it is not.

I am thinking of checking oil pressure next (possible cam phaser or tensioner pulley issue?) and looking for any possible vacuum leaks. Aside from those things I'm at a stand still.

 

I would clean the throttle body and MAF and see if it helps.