Hi there,
Funnily enough the tricky piece of your trip is the Tokyo trip! Aside from that piece, all your travelling looks to be in and around Kyushu :)
This itinerary has really stretched me! How about a 16 day/15 night itinerary like:
3 nights - Kyoto
2 nights - Tokyo
2 nights - Koya san (non-JR trains from Osaka - see our blog post on Koyasan for more)
1 night - Hiroshima (sleep on Miyajima)
2 nights - Kurokawa onsen hotspring (Mt Aso volcano hike on first day before you get to Kurokawa. Use non-JR kyusanko kyushu odan bus to Kurokawa from Aso station. Day trip to Kokonoe bridge by taxi on day 2)
1 night - Kagoshima or Sakurajima. (kyusanko kyushi odan bus back to JR Aso. From Aso on to Kagoshima by JR)
3 nights - Yakushima (by non-JR hydrofoil 'toppy' from Kagoshima)
1 night - in hand to get back to Osaka for your flight
Osaka is a very lively city with a great nightlife, but if you're not city people, then I think you'd get more out of your trip enjoying other parts of Japan.
In terms of Rail Pass cost, a 14 day rail pass will save you a lot of money on this itinerary. The cost of the JR legs for this route would be:
- Kyoto > Tokyo: ¥13220, (161mins, 513km)
- Tokyo > Osaka: ¥13750, (194mins, 556km)
- Osaka > Hiroshima: ¥9950, (103mins, 345km)
- Hiroshima > Aso(kumamoto): ¥13520, (231mins, 449km)
- Aso(kumamoto) > Kagoshima: ¥8910, (152mins, 223km)
- Kagoshima > Osaka: ¥22100, (278mins, 918km)
TOTAL: ¥81,450 for 6 legs
As a 14 day rail pass is ¥45,100 you'd make a pretty great saving with a 14 day japan rail pass over standard tickets. Note this trip does have some unavoidable non-JR legs, specifically the Koya-san trip, the bus from Aso to Kurokawa, and the hydrofoil from Kagoshima to Yakushima.
Many sure you read our blog post on coin operated luggage lockers - for many of your day trips you'll want to leave you heavy luggage at the station. Coin lockers are very safe and can really transform your trip!
Happy to help with any more questions you may have!