Hello Sunil,
I recommend having a look at distances and travel times from Tokyo - Hiroshima and Nagasaki first. While you could visit them in 3 days, you will pretty much only spend time traveling if you do want to include Hiroshima and Nagasaki.
The JR Pass is valid on the Shinkansen to Hiroshima and on to Nagasaki and you can use very good savings over buying normal tickets but again I first recommend looking at the route and see if spending so much time traveling is worth it to you.
To give you an idea, Tokyo - Nagasaki takes 442 Minutes on the Shinkansen.
For Fuji and how to access it, please see our Fuji Blog post.
Hope this helps,
Daniel