Bad Clutch Vibrations After Install

EDIT: Check your throwout bearing for wear. The vibrations ruined mine and maybe yours as well. Hate to see you put it back together only to have that fail on you like mine did! Ha.
My clutch pedal was vibrating for a while too, but I realized that this was only if I put some pressure on it. It I touched it just the slightest (to feel it but no pressure), it felt okay. It got better and better with time (wearing in?). If it seems to drive okay I would ignore it and see how it changes with time. Hopefully that isn't bad advice and good luck!
As for the bolt holes, I'd just run a tap through them and buy some new bolts at a hardware store. Flywheel's aren't cheap.
Torque all 6 bolts down a little bit at a time in a star pattern and throw some blue loctite on the threads.
As for the 22 ft lbs that people swear by, I was never sold on it. The Spec rep I dealt with when I was having clutch problems told me 30-35 ft lbs. Whether you use a torque wrench or not, just be careful not to over tighten and crack the aluminum pressure plate, as FormulaJoe basically already said.
I also tried torquing them to 30lbs, but there was no difference from 22lbs. That is what made me take a closer look at the bolt holes.
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