Ok, here is a strange one. My 2500 Hemi's muffler rusted out. About the same time, I developed rough idling, missing and hesitation particularly at lower rpm. Today it even quit completely. At high rpm it seems to come out of it. Question is, could this somehow because by my straight through exhaust or should I be looking elsewhere? The CEL light has not come on through all this which is kind of strange. The other thing I noticed is that it seems to be worse after you start the truck the second time (warm) rather than when it is cold.

 

Do you still have the cats in place? I would also check your throttle body and clean it. Also replacing the PCV may help too.

 

i doubt muffler would cause it cause i seen guys running no muffller on there trucks and when my old one rusted out i cut the bottom off to see what it would sound like and it didn't do anything different to the truck