Cost effect travel in Japan

Hi there,

I think a 14-day Rail Pass would suit you best. You could start using it the day you travel from Mount Fuji to Kyoto and use it to cover all of your long distance travel up to Osaka and supplement the rest with local tickets and day passes. Don't forget to exchange your Pass when you are in Tokyo as the only possibility to do this around Fuji is @Odawara station.

When you arrive in Tokyo consider using a [Skyliner + 2 Day Metro pass]. It offers really great value, especially if you plan to travel around in Tokyo a lot. For your day trip to Nikko use the Tobu line from Asakusa and is only 1320 Yen for one way!
For your daytrip to Nara just buy local tickets as they are only ¥780 one way.

For onsen:
If you are in the Fuji area consider Benifuji no Yu is a very nice onsen that offers a beautiful view on Fuji-san.

From Kyoto Kurama Onsen is certainly worth a visit too! The area is great for Hiking and after an exhausting hiking trip you can relax in this very peaceful place (of course you can go directly to the onsen too!).

If you intend to hike all the way to the top of Fuji a nights stay is really recommended seeing the rising sun! There are several huts along the trail where you can stay the night but be prepared to pay at least 8,000Yen/person for the night. It is something most people may do once in a lifetime so don't pass it up!

Hope this helps!
-Daniel

Thank you so much Daniel for the prompt reply! Great advice, thank again!