[Jeff Lee]

I have heard of clutch surfaces being machined (improperly) at an angle and accounting for such out of balance numbers as you are reporting. You won't be able to see the problem either. It will also make your runs horribly inconsistent and a vibration. Measure all of your friction surfaces from side to side across 4 corners.
If you find your pilot bearing (I hope you use a bearing and not a bushing) is bad, I wouldn't jump to the conclusion that was the initial problem until I measured the clutch parts.
While on the subject, I've also heard of heat shields being ground but the back side remains warped from excessive heat. That will also cause problems because the friction side has inconsistent depths of material.
And while your at it, make sure your bellhousing to trans mounting surface is still parallel. Years of bolting down a trans can take it's toll on this. And re-dial indicate the run out of everything too.