I will start off by saying that I have been doing numerous searches over the past few days and trying things that others have suggested but I still have a problem.

The problem I am having is that for about the last week the engine has been stuttering. The problem starts upon startup at idle and continues up until 2700rpm. Under normal driving it continues to do it up until 2700rpm but once I come to a stop it no longer does it at idle. Once I get above 50 mph and in 5th gear it no longer does this. The truck has 92k on it and the plugs and cops were done at 90k and were replaced with motorcraft pogs and cops from uneek supply and at the same time the fuel filter was replaced. Once the problem started I did a seafoam motor treatment, then cleaned the MAF, the IAC, and the TB.

 

No CEL?
Could be a low grade misfire..

Check your pcv lines, inspect them fully from front to back of the throttle body for any cracks or collapsing.

Or

If it does it at idle then you can test the cop's and injectors by unplugging the electrical connectors to the cop's one at a time for just a brief second.... Looking for the one that doesn't change the misfire. Unplugging a good cop will make the misfire worse. Then move on to the injectors and do the same.

Theres a misfire somewhere.

What did you use to clean the MAF sensor
When you cleaned your IAC, did you make sure the plunger moved freely and give it a quick squirt of wd40?

Reason I ask, I cleaned one for a friend one time and just with the spray of the cleaner didnt help. Put it back together and same thing, rough starts... rough idle etc. Pulled it back off and realized the plunger was stuck, continued to clean it and work it free. Once it was nice and smooth, a quick blast of wd.... put it back and BAmM, running smooth.

 

It's very possible one or more of your Uneek cops are bad. It happens. Use your old cops to troubleshoot with and Uneek will replace any bad ones on warranty.

 

MAF was cleaned with CRC MAF Cleaner, IAC moved freely without issues, COPs have already been checked along with the plugs, All vaccum lines have been checked and no leaks found
Will check the injectors tomorrow.

 

So the coils were checked at the dealership? That's the only way to check for a low grade misfire. On the WDS or Mode 6 for cylinder history. You can't just check resistance, that doesn't fly. They can pass resistance and still have bad windings, -which 9 times out of 10 is what goes wrong with dedicated coils.

I suppose you should check the EGR valve as well. If it's hanging, it will definitely cause this issue.

 

Took the truck to the dealer today and I would assume they hooked it up to some sort of computer or diagnostic machine but I don't know since I was forced to wait in the waiting area and could not see them working on my truck. The service manager told me that they took it for a test drive and reported that nothing was wrong with it and it didn't miss at all. He then proceeded to ask me what RPM I was shifting at and I said between 2000-2500RPM and he said that was probably the reason it was doing it and that with a manual I should be shifting between 3000-3500RPM. I know he is feeding me BS but he said that unless a CEL pops up there is nothing they can do otherwise. So looking for any help I can get.

 

I just noticed you have a tuner. Have you tried putting it back to stock yet?
Wash your motor lately?
Still seems like a low grade misfire. Or dirty injectors. 2k is pretty low rpms to shift at, and might notice some slight shuttering because of the low rpm. I know my dad always shifts at like 2k and it just sounds like the truck struggles at those low rpm shifts.

 

Dunno about the 4.6, but my 4.2 pulls smoothly shifting at low rpm's. I can floor it at 900 rpm in 5th and it doesn't cough once.

 

tuner has been on truck for a couple weeks before problem started. When it was stock I shifted between 2k and 2.5k and never had a problem. Tuner went on and with the oversize tires I pretty much shift at 2.5k but for the most part I am still at 1.5k once I shift into the next gear. I am going to call some other dealers that are a little bit farther and see what they say.

 

It doesn't matter how long the tuner has been on the truck before the problem started. - Not on bit. So you reloaded with the stock tune before taking it to the dealer ? When you have a problem like this, the very first thing you have to determine, = the tune.

100% confirmation that it's not the tune is a must. Always, unless you definitely know different.

Sometimes you return to stock, go for a drive to test. Then reload your custom tunes and everything is fine again. Computers can get a little flaky,- zapping the pram is like a biatch slap. Just like people, your PCM needs one every now and again.

 

Guaranteed its not the tuner because I have driven it with and without and problems happen both ways.

 

Well after some digging I ended up finding the stock COPs that I took out and using one of them I went in the following order cylinder 1,2,3,5,6 and just kept swapping them with the one factory COP. After each swap I took the truck for a test drive and finally after swapping out the #6 cylider and took it for a test drive the miss is gone.

After driving the truck all day without a miss I would say this solves the problem. After checking the resistance on the COP I took out I found it was fluctuating between 5150 ohms and 5300 ohms on the secondary resistance.