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Tokyo/ Kyoto and Japan Trains and Itinerary?

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I am about to book my air tickets for a trip to Japan and Hong Kong in early September, and I would appreciate any help and suggestions about my plan.

A little background: I have been HK many times, and I like it very much. I have been to Tokyo once and had a "Lost in Translation" experience at The Park Hyatt; didn't like or understand the location (though the hotel was amazing)....battled jet lag unsuccessfully...and just never really connected with the city...my favorite experience was going to Tsukiji Fish market at 4 am, which was easy since I was awake and could not sleep (though I regret not eating sushi/sashimi there). I have been to Kyoto once and loved it.

So I am returning in early September to give Tokyo another chance and to visit Kyoto again. I am planning on spending about three days or so in Tokyo, followed by four days in Kyoto. I would love advice or suggestions about day trips from Kyoto, as well as train logistics. I might be convinced to add a couple of days if it makes sense, but Japan is so expensive, and I am not very amenable to budget travel. In Tokyo I am staying at The Seiyo Ginza hotel, which I think is a very good, central location; is this a good choice?

My current plan is to fly into NRT, stay in Tokyo, then train to Kyoto one way, then fly out of Osaka (KIX) (to Hong Kong for 5 days). Maybe it makes sense to by a railpass if I add some day trips or other destinations? But I understand the railpass does not cover certain trains, including perhaps the Shinkansen bullet train to Kyoto from Tokyo(?). I am particularly interested in a day trip to Hiroshima from Kyoto; is this easy and worthwhile? Does it make sense to spend a night or two in Osaka?

Also, last time I was in Kyoto I stayed at Hiiragiya Ryokan and it was amazing (though pricey), and am considering returning for one night or trying another Ryokan; are there alternatives to Hiiragiya which might be comparable but less expensive?

Thank you.

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