Sorry, this is a long one.
2008 F150 5.4 with 305000KM
Looking for advice on this one, been fighting with this engine for almost a year. I am getting what seems to be a timing issue, but not always throwing codes. Codes it has thrown range from the p0022 to the misfire codes for cylinder #5. For a little background info, this engine was installed just over a year ago, replacing another engine that had been doing the exact same thing, but had some other concerns making it worth replacing. The current engine that is in the truck was out of a junk apparently, buddy of mine gave me it from a parts truck he had bought from a scrap dealer. Before putting it in my truck I replaced all the timing components with a kit from Freedom Racing, the all Ford genuine parts one, new head gaskets, Melling HV oil pump, cleaned the oil pickup, new gaskets all around, exhaust manifolds and spark plugs. I visually inspected the roller followers and the rest of the engine and all seemed good. Motor was a little dirty, but not terribly so. Since installing it, had the same issue as the old one, once warm would and under low throttle it would shake and miss once you were stopped, not bad enough to kill the engine. In the last year, I have also replaced all the COP's (aftermarket, cheap amazon), repaired a spot in the wiring going to cyl. 5's injector, replaced a couple sketchy looking plugs on the wiring harness, replaced both cam position sensors, pulled the valve cover on bank 2 (side with the issue) and replaced the VCT solenoid again (Ford part) pulled the screen from the solenoid and checked it as well as used some air to blow out phaser seeing if there was junk in there as well as pulling the cam cap closest to the phaser and checked it, no scoring and actually shot some compressed air down to blow any junk out of the oil passage leading to the solenoid housing, also went as far as re-replacing the phaser with another new Ford one. Oil changes done every 1500 to 2000KM, using high mileage 5w-20 full synthetic oil while also running Luqui-Moly engine flush a couple times. Nothing seemed to help or change the problem.
Now the weird part. Last week I got home and the truck was acting like itself, running rough when I parked it after pulling in my driveway, so I thought screw it and let it run that way for a bit while I checked some of the wiring and plug ends. Using a noid light I checked cylinder 5's COP plug wire and injector wire, both seemed ok and didn't change how the truck was running when pulled at all. I pulled the solenoid connector and replugged it in, pulled some other COP wires and didn't get a whole lot of effect when pulling Bank 2 ones but it sure changed when I pulled them from bank1. After that I hadn't shut the truck off and had to move it so I revved the engine and it smoothed right out, the smoothest it has ever ran (theres always a slight miss at idle I can feel from startup which wasn't even there). That night the wife and I drove to the city and it ran perfectly, got home(roughly 80 Km round trip with stop lights and 1 drive through), and it was still running great, then decided to be a moron and stepped on the brake and revved it to brake torque the engine and the issue comes back.

I guess this is a chicken and the egg sort of question, is the misfires on cylinder 5 potentially causing the timing issue or vice versa? Also, any ideas on where to go from here? Just looking for some direction, wife will shoot me if I keep throwing parts at it, and I'm starting to feel like a dealership tech doing it that way.
Almost forgot to mention, when monitoring with Forscan there is phaser oscillation when its acting up, none when cold, and O2 sensors seem to read correctly so as far as I can tell without removing them the cat's seem ok.

 

I'm guessing you are getting no DTC's ?

 

It will eventually throw a P0022, seen P0355 a couple times, depending on how long I let it sit and shake for. Also the one that came up last week after it ran so smoothly was the P0020, first time I've actually seen that one come up. I've tried swapping the coils from cyl. 5 to 1 with no change, and mode 6 data always shows a good amount of misfires on cylinder 5 (270+) with a minor amount on cylinder 7 (20-30) when I let it shake for a minute. But on normal times when I hit the throttle to smooth out the engine at the idle right away, it doesn't throw codes at all.
Forgot to mention in original post as well, I replaced the PCM about 3 months ago as well with no net benefit. Should also mention I have run it without the solenoids plugged in and the issue isn't there, but can still feel the minor misfire from startup.

 

P0355 is a ignition coil circuit misfire and you have a lot of them. So you should inspect and repair or replace the pigtail so you know it has a solid electrical circuit and make sure the spark plug is good. Ideally you want all cylinders to be down in the zero or at most 1-2 misfires per drive cycle which is not hard to accomplish in my experience.

The other main thing is switch to 5w30 oil.

​​​​​​ 5w20 is too thin for most of these engines and you won't have enough oil pressure at lower rpms for the vct system to work properly.

Take care of the two above items and you might find things are running much better.

 

Thanks for the suggestions. I'll change the oil over this weekend and see if it helps, and try to track down the misfire.

 

Thanks again for the recommendation. I changed the oil to 5w30 over the weekend, and fixed a couple wires and broken connectors I found. I've taken the truck on a couple longer drives and so far so good, the the truck seems to be running much better. I'll report back if the problem reoccurs and see if we can figure out something else.

 

Kudos. I'm glad to hear it's working out.
And thanks for following up. Its helpful to everyone in the future when threads get updated with progress or hopefully success.