Also check the end play of your prop. Some of the flo torq hubs have slack in them. To fix this most simply grind down the hub center piece so that it eliminates the end play. Just grab your prop and push in and pull out. If there is any play this is probably the cause of your clunking noise.
The clunking should not really cause any problems since there are many Mercury's out there doing this. I however would get rid of it IMO. My Verado does not have the end play problem with my SS Tempest prop but did with the aluminum prop that it came with.