5 day visit

Good morning,

We are planning to fly into Haneda on day 1. We will travel to Yakohama (Narita Express Line) and then spend 2 days exploring Tokyo (for which we will need access to Tokyo Metro network). Then we would like to take Shinkansen to Shin-Fuji and spend a night at a local onsen (will also need access to Minobu Line/Gotenba Line). The following day we would like to take Shinkansen to Kyoto station, where we will be spending the remaining 2 days and will be needing access to Kyoto subway. Lastly we will need to catch The Limited Express Haruka to Kansai Airport. Will all this travel be covered by the 7 day JR pass? Is this the best option for us?

Also, is there an option of upgrading to the Green Car when we travel from Tokyo to Shin-Fuji and from Shin-Fuji to Kyoto the following day (and if so, what is the addition price and how do we do it?).

Many thanks