Maybe warpped rotors and worn pads???
I checked the throttle body the other day, it was still clean. I cleaned it probably 5-10k miles ago. Right now I'm at 55,2xx miles. I checked the fan and the moving parts under the hood and couldn't see any mud. I guess it could be the fan clutch again. I'll be taking it in to northpoint on monday.That clip is just from the factory to hold the rotor in place on the assembly line. Has no other purpose because the rotor will be held in place by the wheel when the lugs are tight. That clip actually HAS to come off with aftermarket wheels or it will cause a pretty bad vibration. How many miles are on your truck?
As for the vibration, I'll quote the pack in asking if you've cleaned the throttle body lately? Though, there are a few other things that can cause vibrations on these such as a fan clutch and even motor mounts. Or since you've been in the mud, do you have any mud all over the fan or any of the accessories? Probably a good place to start is to take off the belt and see if the vibration is still there.