I just got a SPEC stage I clutch put in 250 miles ago. I have this chatter too. At low rpm cruising, the clutch pedal vibrates harshly sometimes . Sometimes at idle, I will here a fast paced "thud-thud-thud-thud" coming from the chattering clutch. If I depress the clutch just SLIGHTLY, the noise goes away and everything is smooth. The fact that the chatter goes away when I push in the clutch means that mechanically i'm sitting pretty.
I also got a burning smell that just seems to be going away. I called spec, and they said it's normal since the clutch is made mostly of metal and kevlar. He said the chatter could be from a unevenly surfaced flywheel, that even if the resurfacing is .005 off from perfect, it could cause some shutter. The flywheel was resurfaced on a machine precisely though, so I doubt it's that. My tranny guy says it could just be the fact that it's a high performance clutch matched with the stangs cable driven mechanical system, and if it was hydrolic it would cure the vibration.
I have accepted the clutch chatter for now, as it's not really that bad, and since it isn't hurting anything mechanically. It's good to know that i'm not in this boat alone though!
-'97 Cobra, rebuilt tranny at 46k, spec I clutch, resurf fly.