does the japan rail pass cover all of our trips..?

Hi there!

The JR Pass will cover the vast majority of your travel, however you will need to purchase some tickets for the last part of your trips to Fuji 5 lakes (Kawaguchiko) and Hakone. Although you can use the JR Pass on all JR lines in Tokyo, you may want to also use the non-JR Tokyo Metro system. There are discount 1 and 2 day passes available to purchase on arrival in Narita.

• For Kawaguchiko, you can use the JR Pass up to Otsuki station. From here you'll need to use the non-JR Fujikyu lines to take you up to Kawaguchiko itself. [Here is a sample itinerary for you]http://goo.gl/SLlme().
• For Hakone, you can use the JR Pass up to Odawara station. From here you'll need to use the non-JR Odakyu lines up to Hakone. I recommend using the Hakone Free Pass, which offers unlimited travel in the Hakone region (all cable cars, funiculars and lake cruise). You can purchase the Hakone Free Pass on arrival in Odawara.

Hope this helps!