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First time trip to Japan in September

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Hi Fodorites :)
My husband and I are taking a two week trip to Japan in late September/early October, and our itinerary is coming along but I have a few questions that I'd be most appreciative of your thoughts on.

Our rough itinerary is:
9/21 Land at Narita at night
9/22 Tokyo
9/23 Tokyo
9/24 Train to Kyoto
9/25 Kyoto
9/26 Kyoto
9/27 Hiroshima
9/28 Kyoto to Hakone
9/29 Hakone
9/30 Hakone to Tokyo
10/1 Tokyo
10/2 Tokyo
10/3 Fly home from Narita in the afternoon

1) We're trying to determine whether to do a rail pass or just pay for the trains as we need them. When we're in Tokyo, we were thinking we could just do a metro pass, for example. And same when we're in Kyoto, and back in Tokyo at the end. The JR rail pass is over $600 per person for the trip...

2) We'd like to stay in a Ryokan for at least one of the nights we're in Kyoto, if not more, however they all seem to be very expensive. Does anyone have any recommendations for one that is under $300 USD per night for 2 people? Seems hard to find. We're looking for a traditional style ryokan not far from Gion. We'd love to stay in Gion however it might be cost prohibitive.

3) We'd like to do a day hiking trip somewhere on our trip. Do you have any suggestions for where to go that wouldn't take us too far from the travel route we're taking? We're intermediate hikers, but really for the fun of it and not avid!

4) Are there any spots you think we'd miss out by not seeing on this first trip, that could fit into our itinerary?

Thank you so much. I'll return the favor in other forums of places I've visited!

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