If all the vacuum lines are good?? Then you could have a sticky poppet valve or leaking fuel pressure regulator, the excees gas getting into the intake makes it difficult for the computer to adjust the injectors and so it sees the truck running rich only on certain cylinders and then tries to adjust the A/F ratio from the O2sensor readings and things get mixed up causing a misfire code in the computer and rough idle...

Get the computer scanned for DTC's, if there are any then you will get closer than guessing to possibilities.