I was having issues with a misfiring cylinder and a DTC for my EGR system, but after new spark plugs and a new DPFE sensor and fuel filter those problems are gone. But I now have another issue that wasn't there prior to the misfire/egr adventure.

When the truck is running and in park or neutral it idles smooth, as soon as I put it in gear the idle get's rough and there are these occasional "shudders" almost as if the misfire is debating whether it want's to come back or not. The rough idle is not present with the transmission in gear and the transfer case in neutral. The shudder's become more frequent the hotter the engine gets. When under light to medium acceleration, or cruising down the highway the engine runs great. There is no CEL or DTC's in the computer.

I can't hear a vacuum leak, but I'm going to pick up a propane torch and some hose tonight so I can start searching for one, I'm also going to pick up a PCV valve if it's in stock. Aside from those two things and a possibly failing fuel pump or CoP is there anything else I should be looking for? I do also know that my battery should be putting out 650CCA but is only putting out about 330 @ ~13v, voltage is good but amps are low, was going to hold off on replacing it until the fall if I could.

I've also read a couple of posts stating that when the DPFE sensor is replaced the EGR Valve should be as well... any truth to that?

 

Not trying to insult you but your thinking is not very good about what your doing.
First if there are no codes there is no vacuum leaks the PCM sensors can detect and you could not normally hear one unless under certain circumstances. No use checking if a leak is not present.
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Second; battery charging is not based on cold cranking amps (CCA).
The battery voltage the alternator detects controls the alternator voltage level and charging amp level into the battery.
If your seeing 13 volts, question is under what condition? Is it while running, after starting or at rest? Makes a difference to the diagnostics.
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Third, a misfire due to a faulty coil does not always set a code.
Smooth idle does not mean the fault is not present; it's just that the motor is not under load until you put it in gear. If you notice your Tach RPM will drop when put into gear showing there is a loading on the motor.
If a faulty coil is the misfire, a Scanner looking at the cylinder misfire monitors will show a high count on one or more cylinders.
Hope i've helped provide a better understanding.
Good luck.

 

No offense taken Bluegrass, I'm just starting to get fed up and my head's going in every direction. Which is the reason I've posted, to try and get this straightened out with the help of more experienced people.

The battery was tested with the truck off, in a parts store parking lot, after the drive to said parts store and a 10 minute wait for a person. Tells me it's the battery voltage, and not the alternator's voltage it was reading.

The problem just got worse and appears to have turned into a full blown misfire under all conditions with no codes..yet. Truck was running as I had previously described this morning, but during my drive back to work from lunch it's become a rough running mess. Now it's just the "shudders" I had described when idling, when cruising, and when accelerating. Much like it was when it was throwing the misfire code... Now I'm wondering if I need to go buy a fuel pressure test kit to check the line pressure.

 

What brand are the spark plugs and how many miles on them? How many miles on the truck and have any of the cops ever been replaced?

Your profile says it's a 2000, can we assume it's a 5.4 because it has cops?

 

Dammit, didn't notice my Sig line is gone, I had the info in there.

It's a 4.6L, the plugs are 2 week old NGK G-Power Platinum's. The truck has 223000KM (138000 miles), yes I live in Canuckistan, sue me :P. It does have CoP's and no they didn't look like they had necessarily been replaced, they were all Motocraft CoP's. As I mentioned when I was troubleshooting a misfire code a couple weeks ago I replaced the plugs. Replaced the fuel filter while I was at it as well.

 

I would suspect those plugs - the Tritons really don't like anything except Motorcraft.

 

Hang in there. We will try to help.
On the battery voltage, it will tend to read high just after shut off if the alternator is working, then slowly go down to around 12 volts as it self equalizes from the normal draws that are present..
After cranking the voltage goes down from the high amperage drain.
The alternator regulator senses this lower voltage and adjust the charge current so the voltage rises as the battery recovers it's charge until a running float is reached somewhere around 14 volts.
A volt meter monitor will show all these actions as a way to tell the health of the charging system.
*
It would be good to test the fuel pressure to see any issue that may be present. Look for a running pressure around 35 to 38 psi to hold well at least 10 minutes after shutdown..
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On the misfire, do use a Scanner to look at the misfire monitors by some one who knows how to do it. It is mode 6, test 53.
Always do the diagnostic work before spending on parts unless you know they are needed.
Hang in there, my rig is over 234,000 miles and still running perfect.
Good luck.

 

Truck threw a code on the way to the parts store, P0301... Bought a coil, replaced it. Purr's like a kitty now, no hesitation, no "violent" shaking. This was the same cylinder that was throwing codes before, until I replaced the spark plugs.

I'll keep that in mind about the spark plugs glc if it becomes an issue.

Goes to show that you need to keep your head straight, I didn't, and started going off on tangents. Should have replaced that coil when it gave me a misfire code the first time. But like they say, Hindsight is 20/20.

I'll still be replacing the battery this fall unless it really gives me issues, 330CCA is not enough for -40 winters