11 Days in Japan, July 2019

Hi,
I am currently organising a trip to Japan for 11 Days with a 7 day JR Pass in July 2019.
We want to visit Tokyo (3 nights), Hakone (mt fuji area) (1 night) , kyoto ( 2 nights), Hiroshima ( 2 nights) , osaka( 1 night) and then back to Tokyo.

What methods of transport would be the cheapest in addition to the 7 day JR pass. Would this include the Hakone free pass or is that not as useful if we are only staying in that area for a day?
Also we have an extra day spare, is there any beaches you would suggest or would it be better to spend an extra day in one of the already mentioned areas?

Many Thanks
Shahani :D