Absolutely right about the JR pass. It is a bargain. Not only gets you from NRT to Tokyo on the NEX, it will also get you unlimited use around Tokyo on the Yamanote Line which you will undoubtedly want to use to most major areas of the city. And in Kyoto there is a JR train to Arashiyama, one of the most beautiful and interesting parts of the area . (If you can find it there is an incredible fix price traditional Japanese restaurant there overlooking the mountain and river up a path into the woods. And don't laugh but the hike up to the Monkey Park there is great fun). So when you add those extras you will definitely save money. Just remember you must buy it here in the US.