Annoying temporary hesitation/skipping
 

So for the past week, my 5.4 3v has been hesitating with a bouncy idle and skipping through the rpms. Here's the interesting part, it only does it after sitting overnight, starts 4 minutes after starting, and goes away after 10 minutes. After that, it's gone and will not come back for the rest of the day even after siting 9 hours while at work for the drive home. The next day, it will do the same thing.

I thought it might be a fuel starving problem of being parked on a hill in my driveway of my new house, but I parked forwards and backward and does it whether I have a full tank or not.

It has 111k miles, I just changed the spark plugs 5k miles ago, and it does have the unfortunate low rpm knocking.

How might I diagnose this problem? Anyone have any clue as to what is causing this? Is something happening in the ecu between 4-10 minutes of run time?

Any help will be greatly appreciated.

-Kyle

*edit*
I'd start by plugging in a code scanner
*end edit*
I'd start by checking your CoP's and their connections. You said you did the plugs 5k ago. Did you rip any of the CoP boots? Did you grease them up real good with dielectric grease when you put them back in?
I'm going through similar right now... only mine is more often, nearly all the time. Slight hesitation at all times, jerking at 45 to 50mph if I give it anything more than a feather touch of gas pedal through that speed. I plugged my code reader in and got P0302 (I think that's the code) that points to a bad coil on cylinder #2. Once I have time I'm going to pull it and test it. If the CoP is still good it will get a good cleaning and new boot and spring.
What is this low rpm knocking you speak of?

Didn't get any trouble codes.. Figures.. I'll start by giving the TB a good cleaning, don't think I've done that since I've had the truck. I'll take the COPs off, inspect, and make sure the plugs are all tight while I'm in there. Would a malfunctioning COP always throw a trouble code? Would it be worth looking at the VTC solenoids as well? Where are those located? I'm due for an oil change as well. I've been using Mobil 1 synthetic for the past year and a half.

What plugs did you use?

Motorcraft.

Your problem sounds SO specific... only after an overnight sit, only from about 4 minutes after start until about 10 minutes...
Oh, yes a bad CoP will give you a code even if it the CEL isn't lit up on your dash.

Sorry I can't be more help, I don't know the start/warm up sequence of our trucks. In general though, a cold engine will run richer while ignoring the O2 sensors until the engine reaches temperature.

New question
 

This is more of new question than reply. I recently changed the plugs in my 05 5.4 3v and it is running worse than it was before (skipping and stalling with very little power) I had to remove some attachments to access the engine. One piece was some kind of fuel piece that sits on the right side of the engine. Not sure if this is the reason. Any help?

Did you replace the COP boots and use dielectric grease?

I did not replace them but I did clean them and put fresh grease on them. They did not look any worse than normal wear. They actually pretty good. Another concern is if they have to go back on any particular cylinder. They weren't marked so put them back on any random cylinder.