These sound to me like several different issues. I would check the flex discs as mentioned above. The down shift clunk is usually an issue of not enough vaccum to the tranny- so look for a leak in the lines or measure what your pump is putting out. There are several good threads on how to do this- including adjusting the modulator pressure. I have had the same issue when my vac pump was dieing.
The vibration is most likely a wheel balance issue.

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