You can put the factory alarm system on a 2000 model bike. And they do work well. Couple of things to be aware of when doing so though.
When doing this on a 2000 you can do it yourself completely as the TSSM won't need to be programmed by the Digital Tech equipment at the dealership to work with the Marelli ECM. The 2000 bike's main harness, however, won't have the connections for the alarm system as does the later year bikes. So along with the security system kit of 68200-00D you'll also need installation kit 68314-01. The installation kit is the interface harness you'll add.
One other thing. The alarm kit includes a bracket to hold the TSSM (the alarm module) in place that is a pain in the ass to use. 70447-01 is the little spring steel clip to hold the module in place that all the later production uses as original equipment. It takes two seconds to install and hold the module firmly in place with rather than the contortionist's act and multiple foul oaths that the stupid bracket with the kit will cause.