Hi Finnie!
I think that it would be best to buy separate tickets for your travel. The JR Pass is pretty neat if you do a certain amount of longer distance travel with it, for instance a return Tokyo - Kyoto quickly pays of. Since you basically go one way Osaka - Tokyo, be it with a couple of really nice stopovers, it would not pay of the use a JR Pass.
As for some tips of what to see and visit:
When you are in Kyoto be sure to visit Kyomizu-dera, this is one of the most beautiful and impressive temples around Kyoto. It is build on the side of a mountain and you can look out over the complete city. Also be sure to walk the streets of Kawaramachi and the close by [Nishiki Market] these places really convey the traditional atmosphere of the city.
In Tokyo I would suggest a visit Akihabara, known for it's gadgets, anime and electronics. It's something you have to see in order to understand. \
Let me know if you have any specific interests and I could point out some more great places to visit!
Enjoy Japan!
Daniel