Shaking can be caused by many things. Here is a list in no particular order:

1. Idle speed too low. Idle should be about 650RPM
2. Clogged air or fuel filters.
3. Valves that are out of adjustment.
4. A rack damper bolt that needs replacing or adjustment.
5. Bad motor mounts.
6. With a cold engine it can be caused by bad glow plugs, this usually goes away after the engine warms up.
7. Imbalanced injector pop pressure or bad spray patterns.
8. Imbalanced compression across cylinders.

A mis-adjusted or bad rack damper bolt usually shows up as rough idle when the engine is hot. I'd start with checking your idle RPM, then replace filters, then adjust the valves. A couple cans of diesel purge will also clean up any build up in the IP and injectors and might also help the situation. Check your motor mounts as stated above, also look at them. Do they look collapsed or broken? If it's only happening on a cold engine they I'd check all your glow plugs. If none of this helps you'll need to rebuild the injectors at the very least, you might just get away with having them re-shimed so the pop pressures are all correct, but you may need new nozzles as well. Then if that still isn't the issue than it's likely that you have uneven compression across the cylinders, which there isn't much you can do about.

Here is a photo of the rack damper bolt.

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