Itinerary check, Tokyo to Fuji to Kyoto

I arrive at Narita July 23rd, then I'm planning on going to Fuji Subaru Line 5th station on the 24th, hiking Mount Fuji on the 25th, then going to Kyoto.

If using the JR pass, what would be the best way to get from Tokyo to the station at Mount Fuji, and then on the 25th getting to Kyoto? Ideally I'd be able to hop onto a bullet train going to Kyoto. If I don't get back down from Mount Fuji until say 13:00, am I still able to leave that day?

Then after a day or two in Kyoto, going to Osaka or Hiroshima, then back to Tokyo for flight out.