Have you considered the JR Rail Pass? You do not mention how you are getting from NRT/HND to Hakone, to Kyoto, etc, but the Shinkansen tickets add up fast and facilitate day-tripping to Kyoto from Osaka or Kobe. Thus you would also have a run of most rail in Tokyo and Osaka as well as the NeX and maybe bypass the need for a flight from Osaka back to Tokyo (which is not all that convenient relative to the train). The only thing you would not get is the private line to Nara.