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Day trips - Kyoto makes a fantastic base camp.
28 mins to Osaka (faster if by Shinkansen, but I don't have a JR Pass unfortunately!),
45 mins to Nara.
Mount Koya is a bit further away, but awesomely photogenic.
I'd also strongly recommend Arashiyama (within Kyoto prefecture). It's famous for it's bridge, bamboo forest and temples, but if you like monkeys then there's a brilliant 'monkey mountain' there too. Bit of a hike but dozens of them are just wandering around, no enclosures.
Personally, I find there's not that much of historical interest in Osaka, so a week there might be quite a while, but the food and shopping are both great, especially near Namba and Dotonburi area (the river neon signs I'm sure you've seen pics of).
Hiroshima - it's pretty small, but certainly interesting - and again, acts as a decent base.
From there I'd recommend Miyajima, easily accessible from Hiroshima, and the ferry is covered by the JR Pass. It's an island famous for it's huge Tori gate in the water, but also loads of mildly insane deer, wild life and walks (with some serious mountain treks if you're keen!)
Miyajima:
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