Originally Posted by fdflys

Definitely skip the flying and use your rail pass. Almost all of your destinations are served by Japan Rail and it's so much easier to just go to the station, find your train and get on. For the Shinkansen's you will want a seat reservation which I believe is included in the cost of the pass. Just go to the station office and they will do the reservation for you. You'll see things from a train that you would miss on a plane. Tokyo -Osaka,Kyoto goes by Mt. Fuji. Many of the places you want to see are close by so you should choose a base (Kyoto or Osaka) for Nara, Hiroshima etc and Tokyo (for Kamakura). No need to drag luggage every day. You can use your pass to go to KIX at the end of your trip. In Tokyo and Osaka your pass is good for the subway loop line. Just show the pass to the conductor when you enter and leave the gates. Relax and enjoy your visit. If you're like most of us who have gone to Japan . . .you will return (and then you can go to more places)