Is the JR Pass cost effective?

Dear Daniel-san,

I am attempting to determine if the JR Pass is cost effective for my itinerary, unfortunately it is too complicated for HyperDia to work out.

Our itinerary is as follows:
1) Osaka Kansai airport to Higashiyama in Kyoto 7th Jan 2020
2) Kyoto Higashiyama to Shinjuku in Tokyo 10th Jan
3) Shinjuku to Iiyama 13th Jan
4) Iiyama to Shinjuku 17th Jan
5) Shinjuku to Tokyo Haneda airport 19th Jan

In Tokyo we will visit Shibuya, Ueno, Roponggi. I am unsure how often we can use the JR pass to get between Shinjuku and these locations?

I was wondering if we can use the JR Pass at all when in Kyoto? Planning to see Gion, North & South Higashiyama, Arashiyama.

There are 2 adults and 1 child.
Are we better to purchase tickets separately or the JR Pass?

Thank you very much.

Regards,
Jen