SO. I'll answer my own question. I got back from my road trip and hooked up my code reader and here they are the codes!
P0208...injector wiring fault
P0308...cylinder 8 misfire
P0300...multiple cylinder misfire
P0316...misfire shortly after start up
Seeing that there was an injector fault, I tweaked the injectors 5-8 (known problem area on this engine)kind of twisting them and unplugging and replugging the connectors. Also moved cylinder 8 coil to 1 to see if the misfire would come back and guess what? It did not! The rough driving and stuttering at 40-60 MPH is GONE! SOMEONE HAS TO ANSWER THIS SINCE THE ORIGINAL IDIOT POSTER DID NOT COME BACK TO POST A SOLUTION!!!
So now I'm back to square one trying to find a solution to the infamous rough idle with no error codes problem that I have been trying to hunt down since the beginning. This was the reason I put all new coils and plugs to begin with.
I also have a noise under the truck that I always thought to be a bad catalytic converter. I took it to a muffler shop and they told me it was not the cats. They brought me over and I heard it myself. The noise is not coming from the catalytic converters but rather sounds like it might possibly be a bearing on the flywheel. The noise goes away with a little acceleration. Ah well. Hope this helps someone out.