You mean the bike is a 2000 thats never been run? or a 2000 with a new top end?
First off if you've got a manual it should explain breakin in detail. If the bike were new the process is a little more involved than for just a top end. Basically everybody will have some sort of ritual for breakin but IMO the idea is to ride the bike for short periods without going crazy on the gas until i feel that everything is working right (usually a tank or two) Having the bike properly jetted is a factor too.
I've never owned a new bike but have done a few top ends without any dissasters.
Hope this helps!
Dave...