Tokyo-Kyoto-Osaka-Kyoto-Tokyo (and some in between)

Hi!

I apologize if this has been asked already, but I could not find anything.

I will be in Japan for a total of 2 weeks during the summer and my friend and I wanted to visit these three cities for sure, and maybe some in between.
For now our planning is as this:

Narita Airport directly to Kyoto: July 17
Kyoto a few days stay including a day trip to Osaka
Kyoto-Tokyo: July 20-21

While in Tokyo we were planning on visiting Hakone or anything close by.

For now we were planning to book a 7 day JR pass, because we plan on traveling mainly during our first week there, but perhaps you have a better suggestion?

Thank you in advance!!

Cheers,
Klimentina