When comparing a new CVO Ultra to a 2000 Ultra, you will have many things to get used to. Besides the compensator and primary issue mentioned by sadunbar, you also have a much higher first gear ratio in the new bike that makes leaving from a stop a little trickier. You may find it necessary to slip the clutch a little more than you were used to on the older bike. And the new bike is probably 150 pounds heavier as well, further amplifying the difference. As for the "tapping" noise sitting at idle with the clutch engaged, that has been a commonly reported issue since the new style primary and the Cruise Drive trans were introduced. I personally think it's got a lot to do with the trans design itself, others have indicated they thought it was a loose primary chain or the compensator. If it bothers you or gets worse, ask your dealer to check it out.
Jerry