Kyoto help

Ahoy there,

Please see our 7 day JR Itinerary and 14 day JR itinerary for our recommendations in Kyoto (and elsewhere in Japan).

I would personally visit Kyomizudera, Fushimi Inari and Nishiki Market in a single day.

Hope this helps,
Daniel

A lot depends on your interests of course!
But the Big 3 to see in Kyoto are Kinkakuji, Kiyomizudera, and the Fushimi Inari Shrine. Fushimi is the most time consuming, and you could spend a few hours to nearly a whole day there if you want:

https://www.youtube.com/watch?v=EandKTAwfOM

Some good guides to Kyoto, grouped by area, are below:

http://www.kyoto.travel/

http://www.ar.jal.com/world/en/guidetojapan/city_information/uky/see/central/

http://www.japan-guide.com/e/e2158.html

Please note that the JR Pass is of limited use within the city. You can use it to go to the Fushimi Inari Shrine and Arashiyama (on the city's west side), but otherwise you'll need to pay for some subways, taxis, or buses.