I am trying to resolve issues that have been going on for a couple years. I've driven the truck very little since this issue came up. I have a 2004 F150 5.4 3 valve, automatic that is from a corporate fleet, like AT&T or something similar. It has 107k miles. It started missing and shaking around 45-50 mph especially when pulling any kind of small incline. After much hair pulling I took it to a local shop that had it for 3 months and never did resolve the problem. Supposedly they replaced the timing chains, tensioners, fazers etc. Showed random misfires that moved from one cylinder to another. The shop never did bill me for the repair. So I don't know if he didn't really do the work he said or he just didn't bill me because he knew the issue wasn't fixed. He said the chains were slack, guides were broken and one tensioner was shot. So I brought it home and let it sit for a long time and now I'm fighting with it again. Currently it is not showing any misfires (since replacing plugs) but it doesn't run well, poor idle. When I drive it it feels like misfires but scantool shows none and no codes. I have replaced all of the plugs, coils, air filter, gas filter, filter on fuel pump in tank, mass air flow sensor, fuel pump control module, O2 sensors, gas cap. I pulled the computer and sent it off to a repair shop that deals with ECMs and they said it was ok and flashed it with the latest firmware. I have an XTool D7 scantool it shows no misfires, 40lbs fuel pressure. It has a power balance test and shows issues with cyl 3 and 5 most of the time. The connectors that plug into the coils have a solid power signal on one pin and a flashing ground on the other pin. I tried adding an additional ground to the engine and didn't seem to help. Suggestions?
UPDATE: Last night I did a smoke test, smoke in the throttle body and it only came out of the oil filler tube. Today I cleared the memory and drove it to reset the ECM. I unhooked the VCT solenoids and didn't notice any difference. Bank 1 vct connector was full of oil. Seemed to run good when I drove it for maybe 12 miles and then started shuddering. When I got back I hooked up the scanner and it showed 1,000 misfires and misfire on #5. On power balance test #5 often drops to minus 30 while #3 will go plus 40 and minus 30 depending if I'm accelerating or coasting. Currently it idles just enough that it doesn't die. I didn't get it today but most days I get a bank 2 lean code.

I'm not a mechanic so I don't know exactly what this means. The bad cylinders are 3 and 5.

 

Post actual codes.
Spark plug boots or COP connectors (not seated) are often the problem.

 

While getting ready to replace the VVT solenoids I discovered a broken connector plug on the driver side camshaft position sensor. After I pulled the plug off the sensor it wouldn't go back in and the latch was gone so it may not have been connecting or intermittently. So I've replaced the broken plug, both VVT sensors and the camshaft sensors. I still need to re-install the power steering reservoir and then I'll test drive it and post back.

 

OK, I got it back together and took it for a test drive. Performance wise it idles rough and had some shuddering around 60mph. Here is what the scantool said.
P0351 primary circuit malfunction of ignition coil A ( I assume this is cyl #1, it showed this before and I swapped coils and tested with an ohm meter, has all new coils and plugs)
P1000 Readiness test of onboard diagnostic systems is not completed ( it always shows this ?)
state of fuel system (open/closed loop) bank 2 - invalid value
no misfires, none at startup or while driving
heated exhaust gas O2 sensors bank 1, sensor 1 and 2 lean ( both banks O2 sensors don't have a thousand miles on them)
heated exhaust gas O2 sensors bank 2, sensor 1 and 2 lean
pip state is high - constantly flashes from high to low and back ?

I'm going to let it sit a while, clear the codes and drive it again to see if I get the same info. Any help is greatly appreciated.
Took it for a 2nd drive and everything is pretty much the same, which is an improvement because I was getting different issues every time I drove it. I also noted that if I rev the engine to maybe 1500 rpm it will be steady for 5 seconds and then it drops slightly for a second or two.

 

How is the fuel pressure, when running it should be about 40 psi under ALL operating conditions? Watch pressure when problem is present, while driving. Key On fuel pump prime value can be as high as 75psi.
Check and make sure the connector for #1 COP is fully seated, needs to snap in place.

 

Fuel rail pressure stays 39-40. I'll drive it tomorrow and observe the fuel pressure on the road. I'll double, triple check #1 cop connector. But if the connection is bad wouldn't it show a misfire? Or does it think it is firing? I'm having a lot of trouble with the little rubber seals in the connectors on several of the plugs. The plugs don't want to seat and the wires are so short they would be a bitch to splice on new plugs. But I may not have a choice.

UPDATE: I ordered 8 new COP connectors and a crimping tool. Because, I can't tolerate half *** unreliable stuff.

 

The codes take a while to set, that is as many as 10 drive cycles before a code will be set.
The COP connectors need to "snap" into place, try removing the red gasket from the ones that will not snap in to place and take it for a test drive.
Depending on where you bought the connectors the new ones may not have new (red rubber) seals. I have a couple of connectors where I removed the red rubber seals to get the connector to snap in to place and have had no issues for years

 

Yesterday I played with it some more. Once I got it to show zero misfires and then it started showing misfires on #5 which I have not been able to cure. I unplugged the coil and connected an old coil not on the engine. It shot a spark out to anything metal within a few inches. I'll be replacing the connector as soon as the new ones arrive. I removed most of the orange rubber seals in the connectors and double checked that they were seated.
The fuel rail pressure stays 38-41 lbs depending if I'm accelerating, coasting or steady speed. Still feel some stuttering around 60mph.
I also ran the power balance and it is showing #3 plus 20 and #5 minus 30. The misfires have always seemed to concentrate on #1,3 and 5. Right now only #5 is misfiring.

 

UPDATE: I found mode 6 on my scantool and #1 seems to have 1 misfire on start up, #5 has hundreds of misfires. At idle I unplugged #5 injector and it made no difference in the engine idle. As I stated above #3 is high on the scantool's power balance test and #5 is way low all the time. I've ordered a set of injectors and will post back when I get them installed.

 

i would suggest confirming diagnosis by swapping existing parts before introducing new parts