This is not a simple thing to check but you need to look for it after all the easy checks have been exhausted.
The first thing I noticed when I got the clutch out was that the pilot bushing was extremely worn. Although it had been many years since I had replaced the clutch and pilot bearing the car only had a few thousand miles on it. So after cleaning everything up I looked at the transmission input shaft. There wasn't any wear on the nose, but it did seem to move quite a bit in the front bearing retainer. I pulled the bearing retainer and could clearly see a crack in the front bearing. So, now seemed like a great time to go through the entire transmission.
I did have the clutch & flywheel assembly balanced with a minor adjustment but I clearly think that the vibration was caused by that input bearing. It sounds reasonable that releasing the clutch would allow the disc to center or release from the rotating mass of the clutch. When it engaged it could move off center and cause the vibration. The car is smooth all the way through the RPM range and I can't tell you how good it feels to have something right that has been wrong for so long.
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