Here is the run down for testing a no spark issue out of my 98 triple manual. I spent all summer testing a similar intermittent ignition issue and in the end, bought a cdi...done. For electrical issues however, I swear by starting small. Just like the manual indicates, wires and connections are your most likely culprits. Good luck.
IGNITION SYSTEM TESTING
In the case of ignition problems, check the following
in the prescribed order until the problem can
1. Sparking/spark plug condition.
2. Electrical connectors.
3. Ignition switches, DESS switch and emergency
4. Ignition generator coil voltage.
5. Trigger coil.
6. Ignition module voltage.
7. High voltage coil output.
8. MPEM voltage supply.