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Train Fares in Japan

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As it stands now, we have the following train rides during our October-November stay in Japan:
1. Narita Airport to Shinjuku Station (we might take the limo bus, though).
2. Kanazawa to Kaga Onsen (25 minutes direct to the town where Beniya Mukayu, our ryokan is located)
3. Kaga Onsen to Kyoto (1 hour, 50 minutes)
4. Kyoto - Nara - Kyoto day trip (Kintetsu line - 35 minutes each way, if we don't stop at Fushimi-Inari Temple or visit a sake brewery along the way)

So, in reviewing the Hyperdia website and the Japan-guide one as well, I see that we can do unreserved seats (presumably purchased at the station), reserved seats (in advance, at additional cost) and Green seats (1st class, also reserved in advance at additional cost).

For my itinerary, what do you recommend?

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