Hey folks, been a long time since I've posted, however, I've been a long time lurker and have always found good information here when I've needed it. I've got a situation going on with my truck and hopefully can get some opinions. I've tried a search and came up empty handed this time.

The truck:

2007 F150 with the 5.4 3v Triton V8

Performance upgrades:

-Roush performance catback dual exhaust (was previously a magnaflow dual exhaust)
-Roush performance cold air intake (was previously a K&N)
-X3 tuner with custom tunes from Troyer Performance

The problem:

While accelerating there is a hesitation. It's only while accelerating and will only do it from a stop, or if you slow down and then take off again. On occasion when its hesitating you will feel the truck surge, lunge, or what feels like slamming into gear and then the truck drives fine. What it FEELS like is a torque convertor going bad, without the flare up. It almost feels like its going into neutral, or missing a gear, and then catching and going. The RPM does not fluctuate when this happens.

I've found that it seems to be more noticeable with the custom tunes installed, however, still does it with the factory setup. It has slowly been getting worse over the last couple years and has started to get very noticeable when towing my trailer with a jeep Cherokee on it (about 7500 pounds combined).

The truck has been to a Ford dealer a few times for this issue and here's what they have said:

-First time the truck was in for other work (I didn't have time to do the work or I would have-they changed rear drive shaft U-joints, rear output shaft seal, rear pinion seal, exhaust manifolds and oil pan gasket) They couldn't duplicate the problem, however, they said there was a power issue and did nothing further

-Second time the truck was in the body shop after some jerk side swiped me. I asked them to have the service people take a look at it cause it was still an issue and they oil pan gasket they just replaced was leaking again
**The specialist went for a ride with me and verified the issue and informed me there was a power issue somewhere and that he did not believe it was a transmission issue. The also did some kind of test and verified that it looked like one of the cylinders was lacking power compared to the rest
**They suggested that the spark plugs could be bad or the COPS could be bad (Spark plugs are replaced every 30K miles, they told me that unless they are factory they are junk and that's likely the problem)

-Third time the truck was in the shop to replace the oil pan gasket again that they still didn't get right. They ended up replacing the oil pan and the gasket. I informed them its still have the power issue and that the plugs are fine and the COPs had been changed
**They said the only other culprit they could think of is that there is a bad injector as per their test it only seems one cylinder is lacking power. They wanted to test each injector and charge me $500 for the test. I told them I would handle it.

The specialist is positive it is a power issue and nothing to do with my transmission due to the fact that it does not flare up when it hesitates. The RPM stays the same

I have had a friend of mine who is also an ASE certified mechanic look at it and he agrees that it is a power issue, possibly an air/fuel problem, and nothing to do with my transmission. However he isn't sure where to look other than sensors as he isn't familiar with Fords.

Maintenance on the truck and what I've done to try to remedy the issue:

-Oil/filter changed every 5K miles with Royal Purple oil and K&N filter
-Sea foam fuel treatment every 5K miles with oil change
-Fuel filter changed with OEM every 15K miles
-Transmission filter/fluid changed at 30K, 60K, and 90K miles (full fluid exchange) with OEM
-Spark plugs replaced initially at 15K with Brisk Racing plugs (recommended by Troyer Performance) and replaced every 30K since with Brisk Racing Plugs
-COPs replaced last year with MSD plugs, after first trip to dealer
-Injectors replaced with OEM after last trip to dealer
-MAF sensor has been cleaned
-Throttle Body has been cleaned and relearn process (or whatever its called) done
-Throttle Position Sensor has been replaced with OEM
****This made an immediate improvement and the hesitation completely stopped. However, it only lasted for one 1 hour trip to Cleveland and then on the trip home it started again like nothing changed.
-Fuel module above spare tire has been changed twice (trip #1 at dealer)
-Fuel pump has been changed once (trip #1 at dealer)

I'm at a loss and not sure where to go next. There are no codes thrown and no lights on (other than the brake light that has been on for about 4 years now that wont go away). This is the first time I have not been able to fix an issue with one of my vehicles simply by knowing how to fix it or looking it up and figuring it out. Other than this hesitation issue, she runs like a champ.

Any ideas would be appreciated

 

Use Techron, not Seafoam.
Use Motorcraft plugs, not Brisk. Those are cold plugs for racing.
MSD coils are not known for consistency and reliability.
Your custom tune must be for that specific intake. Troyer is out of business so you would have to use a different tuner. You can keep the X3.

 

Tune was done for the K&N intake and this issue started while I had that intake. I realized Troyer was out of business when I called to order plugs. Havnt had much time to research a new tuner yet to reprogram the X3

 

Is some one afraid to use a Scanner to look at live data for a clue?
Don't just depend on codes.
A good scanner should have a Trap feature that can be set to freeze a data set at the instant the issue occurs.
It should be able to look at the misfire monitors for each cylinder for signs of a cylinder with a bad coil or intermittent condition.
Look at the fuel trim tables etc.
Good luck.