7 days in Tokyo - Osaka - Kyoto

I have been reading a lot from previous postings, trying to find the itinerary closest to mine and think it is not advisable to get the 7 days JR Pass. But nevertheless, I would appreciate it if you could confirm it or advice otherwise. My travel itinerary is arriving Tokyo Haneda at 11 p.m. As I have read previous postings that it is still possible to try the shuttle bus or train to our hotel Keikyu EX In, is it true?

I did some calculation of my own and it shows that if I get the JR Pass for the following itinerary, it is not worth it.

Day 1 - Tokyo to Mount Fuji and Hakone and back to Tokyo
Day 2 and 3 - Moving around Tokyo
Day 4 - Intend to take the Shinkansen Train to Osaka
Day 5 - Osaka to Kyoto day trip
Day 6 - Osaka to Kyoto or Nara or Kobe day trip
Day 7 - Osaka Kansai Airport

Would I be wasting time if I do day trips to Kyoto. Can't decide whether to stay a night in Kyoto.

I would appreciate your opinion. Thank you!

S.W. K. Lumpur