fuji-osaka-kyoto

This is the tentative itinerary which we've planned. Could you suggest the places we could visit and guide us regarding the accommodation(not too expensive).
Also, would using a JR pass be wise?

Itinerary:
Aug 27 :
By 6.30-7 we reach mount Fuji and begin the ascent. (bullet train)
We reach the top by 3am Max. Thats where we can rest till dawn. Come dawn and we descend, reaching back by 10am. (Japanese sunrise is early !)
Now we can take a direct train to Osaka, or via Tokyo. (This is Aug 28)
Before leaving for Osaka, we book a cheap room to dump all our luggage. Carry only essentials.
There are trains to Osaka every hour, so we do not need to face a lot of trouble. We'll reach Osaka by 2.30-3 PM, and hence take up rooms, where we can rest till 5.
Then we go around for the remaining day, and early morning next day.
We wake up early on Aug 29 and take a mid day train to Kyoto (Its 30 minutes travel).
We reach Kyoto and go around for half a day, taking the most suitable train back at night to tokyo.

A 7-day JR pass would be worth it as you're doing the Tokyo-Kansai round trip, with a stop at Fuji also. Fuji and Osaka/Kyoto within three days is a bit insane I think personally though, you're going to be rushed and will have little time to see anything in Osaka/Kyoto I fear between the trains and your tiredness from Fuji.

Could you suggest the places that we could visit in this span?

If you only have three full days in Japan, I'd probably just skip Fuji, eats too much time, but that's me. Personally if I had so little time I'd do 1.5 days Kyoto seeing the main tourist sights (Inari, Kiyomizu, Kinkaku-ji, etc, dinner in Pontocho if you have the cash and whatnot one night, and then going around Dotonbori or Shinsekai in Osaka the second), half a day in Nara, and the final day in Hiroshima/Miyajima.

Of course the best option in my opinion would simply be to spend more than three days in the country, can't imagine doing such a short holiday overseas myself.