getting around Japan

Hi Maria,

As you already know, part of the way to Fuji is not covered by the JR Pass. Traveling from Tokyo - Kawaguchiko, take local services to Otsuki station using the JR Pass. At Otsuki station buy a normal ticket to Kawaguchiko for the Fujikyu line. Here's a full route.

From Kawaguchiko - Kyoto. Take the Fujikyu line back to Otsuki, from there use local trains to either Tokyo or Shin-Yokohama stations, from where you can use the bullet train directly to Tokyo.

Kyoto and Tokyo are directly connected on the Shinkansen (bullet trains). Also see:
http://www.jrpass.com/blogs/itinerary-tip-mt-fuji

Hope you find this useful,
Daniel