Hello there.
A 7 day JR Pass would indeed be a great idea for your travel to Kyoto and Osaka. The 7 day JR Pass is about the same price as a normal return ticket Tokyo - Kyoto on the Shinkansen, in other words, all the additional travel you will do is what you save.
If I could make a suggestion about visiting Kawaguchiko, consider visiting it as a day trip from Tokyo or otherwise travel to Kawaguchiko via Tokyo, as it is not easy to access from Kyoto/Osaka. My suggestion would be to return to Tokyo from Osaka and then travel on to Kawaguchiko. To travel to Kawaguchiko from Tokyo, travel to Otsuki station and from there take the Fujikyu railway line to Kawaguchiko.
Here is the route from Osaka, if you do want to make the trip in one go.
An alternative is to travel with the Shinkansen to Mishima station and take an express bus from there. This will involve less transfers but cost more as the bus is not covered by the JR Pass. The travel time is about the same, depending on what time of day you travel.
Hope this helps,
Daniel