Tokyo-Shinjuku-Kyoto-Osaka

Hi there!

As the price of a 7 day JR Pass is the same as a return trip from Tokyo to Osaka by bullet, I recommend the following travel tips for you:

1. Purchase a single [Narita Express + SUICA travel card deal] on arrival at Narita to Shinjuku. This will also give you ¥1500 of free metro and JR travel you can use during your trips to Yokohama and Disneysea.
2. Purchase several (up to you, but I guess 3?) unlimited 2 day Tokyo Metro passes for use during your first week. These are a really cheap way of travelling around Tokyo, working out at ¥490/day if you use the 2 day pass. The only catches are that they only work on the Metro (so you'll need to use your SUICA to Disneysea and Yokohama) and that you must buy them at Narita on arrival - they are not available inside Tokyo (at that price)...
3. Purchase a 7 day JR Pass and activate on day 5 until you leave on day 11. This will give you free JR travel up until you leave, including your trip to Odawara (for Hakone), Osaka, Kyoto and trip back to Tokyo and Narita on the Narita Express. Note that for Hakone, the JR Pass will get you as far as Odawara. From here you will need to purchase non-JR Odakyu tickets for travel upto Hakone itself. For day 9-10 you could consider visiting Hiroshima/Miyajima, Nikko or Kinosaki Onsen all for free!

This combination should give you excellent flexibility for your trip, and mean that you save the maximum amount while you are in Japan!

Hope this helps!