Mount Fuji to Kyoto

Hi

I have the following plan with my daughter and was wondering if there will be any JR train from Mount Fuji area to Kyoto:

Jun 28 to Jul 1
Staying in Shinjuku

Jul 1 to Jul 2
Mount Fuji/Gotemba???
where will be a good place to stay
how do i travel from here to Kyoto?

Jul 2 to Jul 4
Kyoto

Jul 5 to Jul 6
Osaka

What kind of pass do I need to purchase?

Looking forward to my trip
Patsy