Tricky schedule - advice needed.

Hi,
Unfortunately for your plans, a JR Pass would not be cost effective. You can get regular fare tickets to take the train (and use the Nozomi, which is faster), or you can fly cheaply on a low cost carrier like Jet Star or Peach. In the Tokyo area as well as Kansai, you could still get some huge savings with regional passes. You have a tremendous time in Tokyo, and you can easily take some day trips to see Nikko, Kamakura/Enoshima, Kamikochi, Izu, and Karuizawa. Using a (or even 2) JR Kanto Area Passes can save a lot. For Kansai, getting between cities is not that expensive, but to go to HImeji for example you could save some using a JR Kansai Area Pass. Other passes that might help are the Kansai Thru Pass if you travel a lot.
In addition, there are other numerous great places you can visit in the area. Okayama is not far and it is famous for its castle, plus Korakuen, one of Japan's Top 3, and also the Handayama Garden. If you'd like to get off the beaten trail for a while, the half day hike up to Konpirasan in Kotohira is stunning. Going to Takamatsu is also nice - it has one of Japan's finest gardens also, called Ritsurin.

Best of luck.