OK. You can probably be better served just getting discount round trip tickets from Tokyo to Kyoto, and back.
The most expensive travel days are:
1) getting from Narita Airport to Tokyo
2) Tokyo to Kyoto
3) back to Tokyo
4) back to the airport.
If you do get a JR Pass:
You can combine three of these day on a seven day JR pass. If you were to activate on day three, the pass would cover travel back to the airport. There are less expensive way to get from Narita to Tokyo, including a Tokyo Shuttle (I usually stay in Nippori, so I take the Keisei private train line).
http://www.japan-guide.com/e/e2027.htmlAs to what to do on the days BEFORE you have an active JR Pass, going to Disney is usually a low transportation cost day. You go to Disney, and then go back to your hotel. It's two rides on the transportation system. Move Disney up.
Other days, where you might go several places on the Yamanote loop (A JR train), you will save more.
As for Hakone -vs- Kawaguchiko, I would look at what places look more interesting to do or visit. Both have private train lines to get to locations, and so the JR Pass is less useful. Look at the two web pages, and decide which looks more interesting to explore.
http://www.japan-guide.com/e/e5200.htmlhttp://www.japan-guide.com/e/e6900.htmlMany people do the "round course" when they go to Hakone.
http://www.japan-guide.com/e/e5210.htmlIf you do this the Hakone Free pass bundles the different transports of the round course into one ticket. You Jr Pass can save you money by allowing you to get the "free area" version of the pass, and use the JR pass to get from Tokyo to Odawara Station and back.
http://www.japan-guide.com/e/e2358_008.htmlFor one of the day in Kyoto, get a day bus pass, to get to many of the attractions in Kyoto.
I usually visit Nara from Kyoto, and stop at the Inari shrine on the way back. Inari Station is between Kyoto and Nara on the JR line.
http://www.japan-guide.com/e/e3915.html If you plan to get the discount tickets:
Use the regular Hakone tickets, and not the "Free area" tickets.
If you are looking for the discount tickets, check out JAPANiCAN to the right add section of Japan Guide. It says "Book Your Trip". After you click on the search button, click on the "Tickets and Transport" button. You will find the Shinkansen tickets there.
I hope this helps,.