1976 Ford Cougar

Transmission problem
1976 Ford Cougar V8 Two Wheel Drive Automatic 57689 miles

I changed my flywheel, but two bolts wouldn't align in the flywheel. Therefore, two of the six bolts are not on the flywheel. Car runs and changes gears correctly. But, when in park, if I idle car up high, car vibrates. When I first take off car vibrates also then stops. My question is, would those two bolts I left off make this happen?
August 8, 2010.

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