Trip review and your suggestion

Hello there,

I am afraid that there is only one over night train from Osaka, which is the Sunrise Express. The problem is that it is often sold out days in advance and you can only make reservations for it once you are in Japan. I would advise staying the night in Osaka and taking an early morning train to Tokyo. Its about 3 hours by Shinkansen and leaving early would leave plenty of time to spend in Tokyo.

Nice day trips to make from Tokyo include, Kamakura, Yokohama, Nikko, Fuji Kawaguchi-ko, and Kawagoe.

Day 5 and 6 look fine to me but be sure to look at transport before hand, getting around Fuji is not the easiest of things.

Now for your questions.
1.) Visiting Kanazawa and Takayama is a great way to spend your time in Japan and this I would not recommending it over something different.

2.) It depends on your final itinerary but starting with a 7 day JR Pass for Osaka - Tokyo - Kanazawa - Takayama - Kyoto/Osaka is a great start. Travel within Kansai does not cost that much, so from there local tickets or perhaps a Kansai Pass would be the best. Alternatively you could add in a visit to Hiroshima and Miyajima and opt for a 14 day JR Pass.

3.) Again, look at transport around Fuji and Hakone. There are a lot of private companies and types of transport here. It can take a bit of time to find the best route. Also consider a Hakone Free Pass if you plan on exploring Hakone a lot.

Hope this helps,
Daniel