Japan Trip 2013

Hi Thaw Sing,

The JR Pass is valid on all JR lines in Tokyo and Tokyo Monorail which cover most of the metropolis, other transport types such as the metro are do not accept the JR Pass.

Going to your questions:
1.) I'd recommend taking the Shinkansen from Tokyo or Shinagawa station to Odawara. This way you get to ride the bullet train which only 35minutes. Odawara is the gateway station for Hakone, from here you can use local transport to explore the area. The bullet train ride to Odawara is covered by the JR Pass but you may have to pay for local transport in Hakone.

2.) I would recommend to make use of a coin locker which are available in large quantities at any station. Some are big enough to store a suitcase. There's also a baggage service at Tokyo Station which can hold on to your suitcases while you explore Japan.

3.) Consider a Hakone Free Pass for your travel there, it covers all kinds of transport and is a great addition to your JR Pass.

4.) This you will have to find out for yourself :)
(I honestly don't know).

5.) To get to Kyoto, return to Odawara station from which you can take a bullet train directly to Kyoto.

I hope this helps!
Daniel