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Many years ago after I replaced the water pump on my 427 I had a minor vibration that took me a while to figure out. I put a dial indicator on the shaft of the fan clutch and saw that there was a wobble in the shaft. I ended up making some thin shims to go between the water pump shaft and the fan clutch shaft until it ran true. I marked everything so that when I took it apart to replace belts that it would go back together without having to use the dial indicator again, since that was a pain. No problems since then. Don't know if that has anything to do with your issue, but I thought that I would mention it.
Just my thoughts-
make sure the brass insert bushing for the fan clutch is not inserted too deep or is too short. This may prevent proper alignment on the water pump shaft which results in a vibration that can lead to water pump damage.