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I have a similar problem for about 3yrs now, but mine is still with stock IMS and clutch on a 99.
Mine always goes away once the engine warms up, but can be reproduce for a very short time if engine cool down just a little, but goes away again once warm. Also it happens even with accessory belt off (so it's not any auxiliary pulley).
I'm interested in this thread and how you will resolve it. I have read that sometimes a slightly loose spark plug can cause this, something to look into (I haven't had the chance and won't get to climb under it until around Mid-July).
Good luck and keep us updated please.
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