First time in Japan

First visit to Japan, I'd like to have my itinerary checked for a couple travelling to:

• 23/8: Arrival in Narita Airport, stay in Ginza
• 24/8: Tokyo
• 25/8: Tokyo
• 26/8: maybe a day trip to Kamakura
• 27/8: Tokyo to Kawaguchi-ko
• 28/8: Kawaguchi-ko and Mt.Fuji (are buses in the 5 Lakes area covered under JR Pass?)
• 29/8: Kawaguchi-ko to Matsumoto
• 30/8: Matsumoto to Kyoto
• 31/8: Kyoto
• 1/9: Day trip to Osaka
• 2/9: Day trip to Hiroshima/Miyajima
• 3/9: Kyoto
• 4/9: Kyoto to Tokyo Ginza
• 5/9: Tokyo Ginza to Narita Airport.

I know that local transport are covered by JRPass in Tokyo, not sure about local transport in the 5 Lakes area, Kyoto, Osaka and the Miyajima ferry.

Thanks in advance for any advice.