Osaka - Kyoto - Tokyo + daytrips - please help :-)

Hello,

Excellent website with lots of information!

I am hoping someone can help with the trip my girlfriend and I have planned for 9 days in May. We fly into Kansai Osaka on 13th May and out of Tokyo Narita on 22nd May.
Our accommodation plans are as follows:
Stay in Osaka 13-16th may
Stay in Kyoto 16-18th May
Stay in Tokyo 18-22nd May

I think a good itinerary will be the following, but I am open to any suggestions/ideas:

13th May Osaka Kansai airport to Osaka central
15th May possible daytrip from Osaka (open to suggestions)
16th May Osaka to Kyoto
18th May Kyoto to Tokyo
20th May possible daytrip from Tokyo (open to suggestions)
22nd May Tokyo to Narita airport

What would be best to do for rails prices? JR pass, or individual tickets?

Many thanks (so excited!!).

Pete