You use a timing like just like you would on a car, but you need one capable of high enough speed for the RPM you're timing at. The Kaw manual says to time the CDI H series bikes at 4,000 RPM, which is 8,000 to a timing light made for 4-stroke engines. Also, you need something like a degree wheel on the crank, with a pointer rigged up, and a way to find TDC, like a piston stop.
The Kawasaki H series manual tells how to time those triples without the degree wheel, using the timing marks on the alternator. I don't remember which triple you have though.
For an inexpensive timing light that will handle high speed:
http://www.kawi2strokes.com/forum/viewtopic.php?f=2&t=133&p=13929#p13929