Re: #4:

The JR pass does not cover any of the Hakone area. It will get you to Odawara, which is the gateway to the Hakone area (on the main Nagoya-Tokyo route).

At Odawara you can purcahse a "Hakone Freepass" from the Odakyu Railroad that will get you between Odawara and Hakone and cover all the bits and pieces of transportation within the Hakone area. Or, there is a Fuji Hakone Pass, also from Odakyu, that is a little different arrangement.

Odakyu has a good English web site: http://www.odakyu.jp/english/freepass/index.html

If you are using a railpass and it runs out before you get to Tokyo, the regular local train fare from Hakone to Tokyo is not very much--I was planning to use a railpass as far as Odawara, at which point it would run out, and I would get a Hakone Free Pass, and then pay my way into Tokyo at the end.

I know all this information because I was planning a trip using a JR railpass and going to Hakone, until I decided to go to Nikko instead, after which I exchanged Nikko for Kamakura . . .