Originally Posted by
worldjunky
... I will definitely eliminate Nagasaki and Hiroshima out of the trip whiles sticking to the rail pass.
You might want to think about Hiroshima which can be done in a long day trip from Osaka or Kyoto. You would want to get an early start and plan on returning in the evening but it can be done. Nagasaki, on the other hand, is on a completely different island and involves 5 hours of train travel just to get there from Osaka. Longer from Kyoto.