Hi there,
The route from Kawaguchiko to Kyoto is unfortunately not very easy. You have three options:
1.) Is to take the bus to Mishima station and use the Shinkansen from there. The cost of the bus is not included in the JR Pass. A one-way bus ticket costs 2,260 and takes about 90 minutes.
2.) A slightly cheaper way with the Japan Rail Pass is to travel by rail from Kawaguchiko to Otsuki on the Fujikyu line (not covered 1140yen / one way) and use JR lines from there to Kyoto. From Otsuki you can use local lines either to Tokyo or Shin-Yokohama station and use the Shinkansen from there to Kyoto.
3.) A third option is to use the bus (not included 1,510 yen, 1h 15min) to Gotemba and use local trains from there to the Shinkansen, like Mishima station and travel from there. Unless you want to visit Gotemba, I would not recommend this route. As local trains are infrequent and multiple connections may be required to get to any Shinkansen station. If you do take this option, then plan ahead!
Hope this helps,
Daniel