Probably should just replace that EGR boot. They sell those at most 3rd party suppliers. When you replace it, don't shove the green tubing in too far or you'll block EGR operation.

 

I did replace the EGR boot. Thanks for the tip on how far to shove it in. I went back and double checked my installation and that tube was probably pushed in farther than it should have been. I'll pull the PCV assembly this weekend and wash it up.

So far, the codes haven't popped back up...but we also haven't been near as cold. The next couple of days should give me a better idea of if I resolved my problems or not.

 

Well...the bad news is we have below zero temps this morning and my sypmtoms have returned. So my problem has not been fixed. At least not in full.
Truck was running fine while warming...drove about 7 miles to where I hit my first stoplight and had to two pedal it to keep the truck running. My RPM's were dipping below 500 and jumping up to 900. It did this at every stop light. I noticed a couple of miles from home a small whine/whistle not nearly as prominent as in the past. I also noticed that when I was driving slowly (~10-15mph) and would let off the gas my RPM's would drop down to around 450-500.
I haven't tripped codes yet...however, I didn't really have time to let it sit and idle until it did this morning.

So now what? Do I just go for it on the intake manifold gaskets and get some other maintenance done while I'm in there? I do have a short list of things to take care of under the hood anyway...

-clean TB
-fix coolant hose connection at firewall
-new plugs

Thoughts? Suggestions on what to test now?

 

I would pull the intake manifold and check replace the gaskets. They are plastic and are known to go bad. Ive changed quite a few along with manifolds. Its a 2 hour job if you really get into it. And you get the peace of mind of having it done.

 

I have been going through the exact same issue for months here in the Chicago area on my 2000 5.4 Triton with 183k miles. I tired everything to clear those codes starting with the cheapest solutions first. Ultimately nothing worked so like you, it came down to the intake manifold. Rather than just replacing the gaskets, I went for replacing the whole thing. They are plastic and apparently known to crack. I figured for the work involved versus the cost (the Dorman version is about $240 at Napa), it was worth it to just replace with a new one. Still have not done the work though (near zero temps and snow up the ying-yang here right now).

One of the last attempts to clear the codes was to replace the plugs. Upon removal they all had tons of oil on them and in two cases the outside of the socket showed signs of antifreeze. It ran perfect for a day and then right back to the same old issues. So the gasket/(potentially cracked manifold) diagnosis is likely the correct one. While looking around I also noticed lots of old greasy oil below the head covers, so since I am removing so much stuff replacing the manifold, I'll also be changing out the head cover gaskets as well. To complete the job, the entire throttle body is getting a deep cleaning spa bath.

If this doesn't clear the codes...the junk yard may be the next stop (and I don't mean to pick up parts). The real problem is that here in the Peoples Republic of Illinois, the EPA won't let you renew your plates until you pass the emissions test and I need the truck for work.

 

The Dorman intake is $163.79 at rockauto.com.

 

To update anyone interested...I pulled the intake manifold a couple of weekends ago. I got all of my parts from rockauto. I will definitely be doing business with them again.
tim1217 - I had the same dilemma...I went back and forth on just replacing the whole intake manifold and being done with it. I eventually decided to just get the gaskets and see what I find when I start digging into the motor. I lined up a loner vehicle from a friend just in case.
So I spend a good portion of my weekend replacing the intake manifold gaskets, put in new spark plugs (amazingly easy with everything out of the way), scrubbed my throttle body, and replaced my heater hoses. I also did quite a bit of cleaning while I was at it.
It has been 2+ weeks and I have no check engine light. My truck is definitely running better. I will say, I did not see an obvious break in the gasket I replaced. I don't know if that is normal or not. I also really looked over the intake manifold for any cracks, or anything that would make me think it was the point of problem.
The temps here have definitely been cold enough for my issues to surface again (-15 this morning on my way to work), so at least for now it appears as though I may have resolved my lean problem. I'm keeping my fingers crossed that it stays that way.