Help Please!

Hello. Im planning a trip for 3 to Japan this december.

Im travelling Osaka -> Nara -> Kyoto -> Gotemba (Fujisan) -> Tokyo.

I was thinking of getting the Kansai Thru Pass for Osaka -> Kyoto. As i think i am able to travel within city with the pass (kindly correct me).
Link: https://www.japan-guide.com/e/e2357_005.html

But i am stuck from Kyoto -> Gotemba. I intend to stay in a hotel between the premium outlet and the station.

I have searched and it said to go
kyoto -> Mishima -> Numazu -> Gotemba.

My question is : Is there a JR pass covering above mentioned? If i get a single ticket, its going to cost me about 12K yen per person.

If possible, I'm looking for a JR pass covering Kyoto -> Gotemba -> Tokyo.

Could you guys also advise me how do i get about in tokyo? Do i buy a pass or do i pay per use?

Thanks in advance!