It could be minor or serious. It sounds to me like there are two things that could be causing it, the flywheel or the clutch itself. The bad thing is the only way to really tell is to take it apart and check out the parts.
If your 45K is soon (say within 5K miles), then I would have them check out the clutch and flywheel. They should check the clutch for wear on the release and pilot bearings and the intermediate shaft and also check the flywheel for uneven wear. If it happens only when you release the clutch (engage the clutch pedal) then it sounds more like a worn bearing to me than other things. They all work together, so an uneven flywheel can put undue pressure on bearings and start wearing them out prematurely. You can have less than 1/2mm of wear on a bearing and start to feel a shudder.
If the clutch has to be replaced, it's expensive, especially if the flywheel is gone too. I'd take it to an independent shop and see if there are aftermarket options to the flywheel. The dual-mass flywheel that comes in the 2000 is troublesome and cannot be machined flat. The part is over $700 itself. Clutch installed I've seen on here up to the $4K range.
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