Tokyo Hiroshima Naoshima Koyasan Kyoto Tokyo in 15 days

Hi there,

I see that you already have done a good amount of research and you are correct that with your current plans buying tickets would be the better option. I think the best way to use the JR Pass is for long distance travel and you can make some really good savings if you do. You kind of take this purpose away, because of the travel by night bus to Hiroshima.
With the JR Pass you can completely avoid the night bus and enjoy a much smoother journey. It would also pay off getting the JR Pass if you would travel to Hiroshima with it.

Here is a little list of ticket prices to illustrate what I am trying to say:
Tokyo -> Hiroshima ¥ 18,050
Hiroshima --> Uno (for the ferry to Naoshima) ¥ 6,180
Uno --> Osaka (for Koya san) ¥ 6,690
Kyoto - Tokyo ¥ 18,050
Tokyo - Handa Airport ¥ 620

For a total of ¥ 49,590, or ¥ 4,490 as the 14-day JR Pass is ¥ 45,100. Of course you can also use the JR Pass for local JR trains in Tokyo and around Kyoto. I guess that it really comes down to taking the night bus, personally I try to avoid them because I can never sleep in them and lose the next day due to fatigue but there are enough people who are completely fine with it.

I hope this puts things a little in perspective.
Daniel