Yep, as said before if it is a manual it is probably because of the dual mass flywheel going bad. My truck is a manual and I'm pretty sure I still have the stock DMF with 273K on it...when I shut it off it shakes a little but you can hear something loose rolling around inside the flywheel for about 5 seconds haha. I'm going to get a Valair clutch and a solid flywheel conversion soon.
Check your engine and transmission mounts, the manuals do not shake much more than an auto unless they have an issue, I've driven them with a single, dual disk, and the stocker, they don't shake hardly anymore than my auto.
My manual truck didn't rattle at all when you'd shut it down, just a little shake.
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