it's highly unlikely that the jetting has anything to do with it. It's a 19 year old bike, which means it's probably wear and tear that needs to be addressed.
Start with the basics :
- Clean the carb, all the internal jets and set the float level (but leave the jetting alone for now)
- Clean and oil the airfilter. If it looks worn get a new one.
- Adjust the valves (chances are good this will go directly to your issue)
- Put in a new sparkplug
- Clean the electrical connections, the coil wire, the coil wire ground (very important)
- Do a compression check.
Once you do the above basic maintenance things, then start troubleshooting.
A Yamaha Clymers, or Haynes service manual will show you step by step how to do this maintenance and provide a troubleshooting chart if you have to look further.