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'06 4wd F250 Diesel CC 20" rims short bed. I had an issue with the vibration around 40 mph fixed and it was the tires. The thing I still notice now is when I turn I feel like I am going over bumps while turning. This happens even on smooth level surface. The type of turn is when I am at a stop and make a left or right hand turn.
Could be the slip joints on the driveshafts are a little sticky causing a popping noise. I think there is a TSB out on this. Look above in the TSB/recall section.
I'd definately say its the LS. If you want to do it yourself the first thing you should do is to check the rear diff fluid to make sure its not low or contaminated. If everthing looks fine then you'll need to get LS or Posi fluid (Friction Modifier), just start by putting in just a little (my '99 SD DRW with the Dana 80 only takes 8 oz total), take it in a big parking lot and do a few figure eights and see if the "chatter" goes away. If not try a little more, but don't go overboard because adding too much will cause your axles to act like an open axle. Mine was just starting to chatter a little so I had the rear end flushed and refilled with new synthetic gear oil and friction modifier (it was due anyway) and now it turns smooth as glass. Hope this helps.