Hi there. We have an 01' F-550 7.3L with a rough running issue. It was previously running rough only on hotter days, after warmed up. Fast-forward a couple months & now it runs poorly when first started cold in the morning. Here's what we've done so far:

1 year ago: We replaced injectors with reman units from Ford. We also replaced the valve cover gaskets that include the wire connections, plus we bought the injector wire pigtails from Ford and replaced them as well. It ran fine for the last year +.

1. Cyl. #3 temp measured at exhaust manifold 100*F running at idle cold in the morning, all other cylinders 145*F or higher.
2. Compression check: All holes at 350 psi - 400 psi.
3. Checked resistance on injector wire harness at IDM connector...no resistance/circuit issues based on tests.
4. Pulled injectors and sent them out for testing - all injectors passed all test.
5. A friend of one of our mechanics came by with a SnapOn reader & checked out the high pressure oil pump. I can't remember the details now, but he said it our HPOP wasn't the problem. I can get better details if needed.
6. We replaced the fuel filter/pump that is in the fuel tank. The original one was nasty dirty. We also replaced the fuel filter in the housing under the hood.

I'm not sure what to do from here. Looking for direction.

Thanks,
Nate

 

That 42 pin connector over the drivers side valve cover, take it loose (10 mm bolt holds the connector together) and swing the wiring harness which runs down the side of the engine, away from the valve cover. Look for chafed wires from rubbing against the outboard side of the valve cover. The split poly wire loom (plastic cover they put over the wiring harnesses) tends to slip down, and the wires rub the valve cover, chafing the wire insulation.

I'm not saying that's the problem, but it could cause your symptoms. The best part is; its not rocket science to check it, and repairing it is really cheap.

 

We will take a second look at it, but I thought if we had an injector wire harness issue, it would have shown up when we did 3 tests to the harness.

1 - We checked resistance between power feed & each injector's ground circuit at the IDM connector....all were within range between 2.9 and 3.1 ohm.
2 - We checked to see if an injector circuit was shorted to ground....resistance checks at each circuit were all OPEN...infinity....no path to ground = OK.
3 - We checked resistance between each injector power feed and the ground shield for the injector wires....all OPEN circuits...infinity....no path to ground = OK.

Like I said....we will do a visual again...thank you.

 

This is the wiring that comes from the chassis wiring harness to the engine wiring harness connector - the outboard side of the drivers side valve cover.
I had very similar symptoms and that was the cause. Drove me nuts for a while!

 

Did you have any luck?