Had a funny idle this morning. I have a 2.2k ohm resistor in my iat sensor but I dont see how it would have anything to do with it. Cranked up and drove to work this morning and all was fine. Got in my truck a couple hours later to go to my next store and truck cranked up and idled fine a few seconds then it idled to about 950 or so then back down to 800. It did this on and off for a minute until I put it in drive. Then got to my next store and it was doing the same thing when I parked, it would idle like this for 3-5 seconds high then 3-5 seconds low. I reset the apps and then came back out in a few hours and the truck was doing the same thing. Next store I reset the apps and it has been fine since. Not throwing any codes either, any idea's?

Try pulling your MPG fooler temporarily and see if it is causing this effect...

Well with the warmer (70+) I havent had any trouble but it got cold (50) over the last couple days and its been acting up again. I pulled the 2.2k resistor and hooked the iat sensor back up and it didnt change anything. I noticed when its cold out, my alternator stays down around 12v when im idleing but then gets up to 14 when I start driving. When the truck idles itself up the volts rise and then they fall when it idles back down. I resset the apps several times yesterday with no luck but after it warmed up in the afternoon it ran fine. Maybe a bad alternator?

Try having the alternator bench tested and make sure to have them check the diodes for function. Just because voltage is present doesn't mean it not leaking AC current through 1 diode which could be enough to drive the ECM, PCM and VP44 nuts...

I will, also got a 1688 today but I erased it and it hasnt come back. I bet its the alternator. My temp gauge is also fluctuating sometimes, it will never get up to temp and fluctuate from 160-180 or so, seems like this idle is crappy when this is going on too. I have heard that cummins has a new thermostat to fix this issue so I ordered one. I think he said it was a 83 (181.4 f)degrees celcius t stat but as far as I know, mines a 190.