Hello Hyde !! I'm glad to read your plan, coz it's very similar to mine
Use this to know the distance between cities
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I was intending to get JR pass, but I think I could save a lot of money with seishuun 18 kippu (and also considering that I'll be using city pass). For Hakone, there is also 2 day pass, so practically the only thing not covered is my return trip from tokyo to kyoto.
Will you be attending Anime Fair on 30th march? We can go together ! I'm hoping one of my fave seiyuu's gonna be in this event
I'm also at lost when it comes to food, probably I will do a random pick =_=
This is what i use to find accomodation :
Hostels & Youth Hostels Worldwide - Online Bookings