Visiting Japan, Osaka and Kyoto

Greetings,

My husband and I are travelling to Japan on 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 03 - Arriving Narita Airport at 05:05 pm, we plan to stay at Shinjuku/Shibuya area.
April 03 - 09: Tokyo (6 nights, 7 days)
April 09 - 13: Tokyo to Osaka (4 nights, 5 days)
April 13 - 15: Osaka to Kyoto (2 nights, 3 days)
April 15 - Kyoto to Narita Airport, our flight departs at 07:50 pm.

Since April 15 is our 13th day, please note that our 1 week JR Pass has expired.
Any advice will be greatly appreciated.

Thank you very much.