Firstly, you might buy a 14 day Japan Railpass for 45,100 yen, or 450 bucks in order to do a Tokyo-Nagano-Hiroshima-Matsuyama-Osaka-Kyoto-Tokyo tour in 14 days.
http://www.japanrailpass.net/eng/en003.htmlYou cannot take the Nozomi on Tokaido Shinkansen on the pass.
Individual ticket prices and model connections:
1) Tokyo to Nagano: 7,970 yen each way (reserved seat)
Tokyo 8:16 - 10:00 Nagano
2) Nagano to Hiroshima: 17,150 yen (reserved)
Nagono 6:10 - 9:16 nagoya 9:46 - 10:53 Shin-Osaka 10:59 - 12:28 Hiroshima, or
Nagano 9:00 - 11:59 Nagoya 12:11 - 13:44 Himeji 13:49 - 14:52 Hiroshima
3) Hiroshima - Matsuyama: 10,660 yen (reserved)
8:15 - 8:57 Okayama 9:24 - 12:11 Matsuyama
4) Matsuyama - Shin-Osaka: 11,170 yen (reserved)
Matsuyama 8:11 - 10:59 Okayama 11:33 - 12:24 Shin-Osaka
5) Osaka - Kyoto: 540 yen
Take the new rapid service train. It runs every 15 minutes and takes 28 minutes.
6) Kyoto - Tokyo: 13,220 yen (reserved)
Kyoto 8:29 - 11:10 Tokyo
Secondly, as for transport between Narita Airport and central Tokyo, I'd recommend the follwoing way.
a) ex-Narita Airport:
Buy a 'Suica and NEX' package for 3,500 yen. This comes with a Narita Express ride to central Tokyo etc and connecting train rides within the Greater Tokyo Area, in addition to a suica card (500 yen deposit) with 1,500yen credit.
http://www.jreast.co.jp/e/suica-nex/index.htmlb) Returning to the airport from Tokyo:
Take the Keisei Skyliner or the limited express from Nippori. The former costs 1,920 yen and takes 55 minuts and the latter costs 1,000 yen and takes 70 minutes.
http://www.keisei.co.jp/keisei/tetudou/keisei_us/top.htmlNo Airport-bound NEX discount ticket is available. That's why I recommend you to use the Keisei Line.
Thirdly, I'd like you to be oriented in transport in Tokyo.
Various one day tickets available for getting around Tokyo.
http://www.jnto.go.jp/syd/pdfs/USEFUL_TICKETS.pdfThe information is partially outdated in that Passnet is no longer available, being replaced by 'PASMO'
http://www.japan-guide.com/e/e2359_002.htmlOne day tickets can be bought through the suica credit at a vending machine at any train operator station, except the Tokyo Metro Open Tickets, which must be bought at NRT.
Tokyo transport orientation:
http://www.japan-guide.com/e/e2017.htmlTokyo Metro Open Ticket (one day: 600 yen, two day: 980 yen)
http://www.tokyometro.jp/global/en/ticket/narita.html#narita...Lastly, in central Kyoto and Osaka, the JR pass is nearly useless. Therefore you might buy one day unlimited tickets in each city if you get around a lot.
http://www.kotsu.city.osaka.jp/foreign/english/ticket/index....http://www.city.kyoto.jp/koho/eng/access/transport.htmlHope this helps.