Will the engine shake more violently the more miles you have on it, and the more broken in it is? Thats one thing I love about my cummins, that shake!

 

UH- - - - Really depends on when you shut the truck down during use. I know that giving it a little throttle right before I turn the key to the off position it makes the shake less noticable!

 

not sure about more shake but i have a 06 6sp and when i have the clutch engaged and turn the truck off it doesnt shake as much as it does with the out?

 

If by "clutch engaged" you mean "the pedal is pushed down", then technically the clutch is DISengaged because the transmission is not connected to the engine.

I agree that when the clutch pedal is pushed in during shutdown (DISengaged) there is less overall shaking. There's also a discussion on this site that holds it's better to have the clutch disengaged (pedal pushed down) during engine shutdown because it's easier on the clutch/transmission due to torque spikes. Might be more important with the 2006 dual-mass flywheel, I'm not sure.