Is JR Pass best for my trip

Hi there!

To start with your last question first, the JR Pass is pretty amazing if you use it travel travel around Japan a lot. For instance a return trip Osaka - Tokyo will quickly pay off. From reading that you only plan to go one way Tokyo - Kyoto/Osaka I think that it will be smarter to buy normal tickets. However a JR Pass would quickly pay of if you used it for a day trip to Hiroshima for instance.

If you do get a JR Pass, the JR Office at Narita airport is open until 9.45 pm which should give you enough time to exchange / activate your JR Pass. Than when you travel to Kyoto on day 4 you can take any Hikari or Kodama shinkansen heading toward Kyoto. Just ask the JR Staff where you wish to go and they will find the right route for you.
You can either travel from Shinagawa station or Tokyo station because the Shinkansen stops at both.

I hope this helps!
Daniel