I have an 06 SCREW 5.4l 4X4 with the only mod being a Flowmaster 30 Series muffler and an Evo programmer. I have begun to notice a slight vibration/miss/shudder/rough idle (yes, all that, it seems) some times while either first starting it up at idle or after driving for several minutes/miles. It almost reminds me of how a 2 cycle bike feels when a plug gets fouled, but not as obvious. I am under the impression that if a plug were fouling it would trip a code, but I have no lights or code alerts. There seems to be no rhyme or reason for why this is happening. The Evo is set at level 3 and I use 93 octane fuel. I tried returning the Evo back to stock settings and drove it for a few days The problem never reoccured, but it is so infrequent and I hate the way the truck runs on stock settings vs. Level 3, so I changed it back after a week to level 3 again. I checked the Evo for an update and it said none were found. Is anyone aware of something that may be causing this? I am not sure what to do from here, but I can't even imaginee the cost of having someone trace it or try to troubleshoot. Thanks for any input. This is a great forum!

 

Could be a misfire on a cylinder which wouldnt be very noticeable when there are 7 other cylinders, or it could be a vaccum leak.

Had something similar to this on my 2001 WS6 Trans Am after taking it out of storage for 2 years and it was a leak on the PCV Line. Replaced the hose and runs great now. Depending on how many miles your truck has these are my best guesses.

 

^ one cylinder missing is very noticeable. It could be many things but I'd wait for it to get worse before trying to fix it. And my truck has a terrible miss right now and it won't throw a code.

 

Well I guess I'm not the only one with this issue... Thanks.