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Oh, also consider unplugging the maf and map and see if anything changes as far as codes setting for the pedal. If one of those are bad, it could mess up the APP readings to the PCM.
What's really weird is when it is running like crap and chugging and jerking if I set the cruise it will clear up and run smooth and if I clear the codes 99 % of the time they will not come back until I shut off truck and restart even though truck is running bad
The cruise control essentially causes the PCM to ignore the accelerator input and determines power output based on the cruise set speed and your actual speed, so that makes sense in a way.
There is some intermittent short or break in the wiring that is causing this problem. When the PCM detects one of the APP tracks out of range or disagreeing with the other two, it sets the code and the MIL (even thought the manual says it doesn't set the MIL it actually does). As long as two tracks agree it will continue to run normally. If all three APP tracks disagree the PCM defaults the engine to idle.
Since you're not being defaulted to idle, you have to assume that whatever is causing the problem is very intermittent. It's happening long enough to cause the engine to stumble and to set the codes.
I think you are probably on the right track by replacing the harness. Unfortunately, intermittent electrical problems are a bitch to track down and fix.
I did, and it might be worth checking out. But since it appears he is showing symptoms of actual APP problems (engine stumbling and dropping to idle), I discounted it a fair bit.
Otherwise it has to be a wiring problem between the pedal and PCM. What I would do is make a jumper wire and jump each wire going from the pedal to the PCM. One at a time, and see if you eliminate your problem. Check all the wires carefully near the connectors, they can break internally and only be kind of connected. You will feel them being "stretchy" from the sheathing.
Since you are looking for more ideas and you have not mentioned connector C-145 which is located by the battery junction box. I would pull it apart and check it out to make sure there is no corrosion in there. The signals for the pedal go through this connection.
Sorry my mistake on the year. I am curious though is your truck an early build and more like the 2003 or a later build that has the later 6.0l engine. I am just wandering if the wiring harness changed some where mid year. I looked at a 2005 print by accident and the accelerator pedal Pots go through connector C145 instead of the ones you posted.
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