JRPass

Hi there,

For a trip like this I recommend you look at passes and deals for the respective metropolitan areas and purchase a single bullet train ticket between Tokyo and Kyoto (¥13,520).

For Tokyo, you should take a look at the Narita Express/Suica Metro card deal, or the Tokyo Metro 2 day travel pass + Keisei Skyliner deals to save you money on your travel from/to the airport and around Tokyo.

For Kyoto/Osaka you should consider the Kansai thru pass. This pass covers most non-JR travel in the area, which includes local buses and metro/subways in Kyoto and Osaka and transport to Kansai International Airport. Here's a map if the Kansai thru pass coverage for you.

Hope this helps!