Hi there,
For Nikko, Nara and Hiroshima, your best bet is getting the bus from the station. In Nara, it's unlikely you'll even need it as most things are within walking distance, but in Hiroshima, chances are you'll have a much easier time by getting on a bus.
As for prices, you can get a pass, or simply hop on. In my case, I've always hopped on buses and paid the fair - this way I can spend as much time as I like at each place, and not feel like I've got to move on to make the most of the day pass.
Japanese buses are easy to get on, but it can be tough to know which stop to get off on so keep your eyes peeled!
Best,
J
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Japan Rail Pass - buy the JR Pass online
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