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Well I got Torque and imported your CSV. I am new to Torque so I wasn't quite sure how to create the display you showed but here is my best shot:
After a few 5 mile trips this is the worst case misfires. What has been done so far:
Tensioner Timing Chains
Belt - Timing
Sensor Camshaft Position
VCT Solenoids
All spark plugs
One coil (cylinder 4)
Cleaned throttle body
Cleaned MAF
Fuel filter
Air filter
New oil and filter...
The slightly rough idle is intermittent but enough to notice for sure. I haven't had the truck very long and I have had to add a quart of oil. I didn't check it when I got it back from the garage so I don't know for sure they filled it. I will monitor oil and gas use from here on out.
You did good on the Torque dashboard. Defonately got a few misfires, but seems just at startup. Torque Defonately gives a good Mode 6 report.
You should be able to expect smooth idle with the work done on your truck
You mention the problem is worse when it warms up. Did the dealer replace guides and/or drop pan to remove debris when they replaceed chains & everything?
That's a good question. I don't know the answer. I will look back at the invoice and see if it has a pan gasket listed. I still have the original COP boots and injectors, that is next on my list. I don't have a heated garage so that may wait until spring!
Finally got a somewhat warm day in Illinois so I replaced all the injectors (motor man injectors) , all new coils and boots (AutoZone) this weekend in the driveway.
Here is what has been done so far:
Done by the Ford garage:
Tensioner timing Chains
Belt - Timing
Sensor Camshaft Position
All spark plugs
Fix rear pinion seal leak
New rear brake rotors and pads
Local garage:
VCT Solenoids (Motorcraft)
Both catalytic converters
Done by me:
Fuel, oil and air filters
All coils and boots
All fuel injectors
Clean throttle body
Clean maf sensor
The good news is there is no engine rattle whatsoever and the truck seems to have plenty of power. The bad news is I still have the original problem of an intermittent rough idle. Now it seems to be more predominant when engine is not warmed up. I did get some codes this weekend. P0300 and P0316, random misfires. After a bit the engine smooths out and no more misfires. Sometimes there is no problem at all. I have attached a .csv file of fuel trims, maybe someone can make sense of that.
Some days there is no problem, other days it runs rough until warm. Frustrating after all that has been done. I would not have sunk this much cash into a 2005 vehicles but this truck is a 5.4L 3V XLT 4x4 with zero rust and is in great shape otherwise. It has 130K miles on it.
I haven't been able to find a vacuum leak of any kind and I just don't know what to do next.
Did a couple of 3 or 4 mile trips and watched for misfires. Did not get many. I need to do this when it is acting up but not sure that would tell me much. With new injectors, coils and boots I don't know what else would come into play except maybe vacuum leaks, intake manifold cracks or gasket leak. Kinda stumped at this point.
The timing job including VCT solenoids is fine, I have no ticking at all now. New CATS are not throwing any errors and seem fine.
It all comes down to a cylinder one misfire upon cold start. I have yet to wire in new pigtails on the #1 cylinder injector and coil. My next step is to replace coil 1 and injector 1 and new pigtails. If that doesn't fix the problem then I suppose it could be a vacuum leak, intake manifold gaskets or worse a problem with compression on that cylinder.
Truck cranks fast (good battery) for a few seconds then runs fine. Torque Pro always shows cylinder 1 misfire upon startup then I can drive any distance and no more misfires on any cylinder. The problem is just when the engine is on startup. I did replace all coils, cops, boots, injectors. I couldn't afford Motor Craft injectors or coils. I used AutoZone coils and boots and I got the injectors from eBay (they look identical to the ones I took out). I got them from Motor Man Fuel Injector Supply ( 5C3E-DC Flow Matched Fuel Injector Set (8) Ford Truck & Lincoln 5.4L).
I do think I may have noticed a fuel smell upon start but not sure.
Ford's PCM logic categorizes misfires into a couple of categories of severity. Sounds like your's is down the list pretty low - even though my experience proves you can ultimately get rid of practically ALL them. Those before the first 200 revolutions will show up on the Torque Pro 'misfire' screen -per cylinder count and the total cylinder count. Those are the Mode 06 individual cylinder counters for the Current drive cycle - which are 'exponentially' weighted into the count for the last 10 drive cycles - so it takes quiet a few before they begin showing up.
But only those occurring AFTER 1000 revolutions will reset the Freeze Frame Data and clear the number of Drive Cycles since the last misfire (MFF_0_CNT) Pid # 2216DC, equation (A*256)+B. My truck will register a couple of the lower priority ones if I turn key on for about 30 seconds before hitting ignition --- (I think likely is an injector that weeps a drop or something) However it is not uncommon for mine to rack up 50- 60 or even 80 drive cycles before MFF_0_CNT gets cleared (a post 1000 rev misfire). Then you can tell by the Freeze Frame pids what the prevailing conditions were when it happened.
It sounds to me like you could have a leeky injector on cylinder one.