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Does it do this when stationary, or just when moving?
At what sort of speed, or all speeds?
In what, or all gears?
Under acceleration, deceleration, cruising or all three?
Did you change the engine mounts? Maybe they are knackered.
Yeah check ur engine mounts if u didnt change them also check ur fuel supply right from ur injectors to ur tank. If u have a leak it could also suck in air (causing ur engine to run rough or cut out). Hope this helps but i am a diesel mechanic and i am going on what i know about diesel engines. Have u had an aftermarket fuel pressure reg fitted at any time?