Easiest way to spot a 1999 or a 2000 Hayabusa is by looking at the lower section of the side fairings.

The '99 does not have an extra bolt about 8" back from the front lowest fairing bolt. The 2000 does. (I presume the 2001 does as well, but they are distingushable by their different paint scheme)

The reason for this bolt is to hold the 2 parts of the fairing together as they warp under the heat from the exhaust headers.