13 Days in Japan

Hello,

My wife and I are travelling to Japan from April 3 - 15, 2014 (12 nights, 11 days) and will be flying
in and out of Narita airport.

We want to visit Tokyo, Osaka, and Kyoto and need some transportation advice to plan our trip.
We do plan to buy a 1 week JR pass, but since it does not cover our trip time span, we need some
advice/help to plan our travelling wisely to maximize the use and minimize our transportation costs.

April 3 - Arrival at Narita Airport at 05:05 pm, we plan to stay in Shinjuku/Shibuya area.
April 3 - 9: Tokyo (6 nights, 7 days)
April 9 - 13: Tokyo to Osaka (4 nights, 5 days)
April 13 - 15: Osaka to Kyoto (2 nights, 3 days)
April 15 - Kyoto to Narita Airport to catch our flight at 07:50 pm.
Since this is our 13th day, please note that one week JR Pass has expired.

Any advice will be greatly appreciated.

Thank you very much.