Hi there,
Overall I like your trip - Here are some thoughts:
- The trip from Kansai Airport to Naoshima will take 3.5hrs, so you may want to spend at least an overnight in Osaka of Kyoto depending on your flight length.
- Kanazawa is a great location - rather than heading back to Kyoto, how about overnighting there and then travelling up to Tokyo the day after?
- Hakone is on the way to Tokyo from Kyoto. Rather than doubling back on yourself to Hakone from Tokyo, consider stopping off at Hakone on the way up to Tokyo to save further time on trains. Note that for Hakone the JR Pass will take you as far as Odawara. From here you'll need to use the non-JR Odakyu lines up to Hakone itself. I recommend the Hakone Free Pass for this.
As for prices, lets see how the JR ticket costs for your first 7 days stack up against the 7 day rail pass at ¥28.300:
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Kansai airport > Uno: ¥8,580 (228mins, 273km)
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Uno > Kyoto: ¥8,580 (139mins, 252km)
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Kyoto > Kanazawa: ¥6,910 (124mins, 224km)
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Kanazawa > Kyoto: ¥6,910 (126mins, 224km)
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Kyoto > Tokyo: ¥13,420 (161mins, 513km)
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Tokyo > Odawara: ¥3,840 (35mins, 83km)
JR ticket cost: ¥48,240 for 6 legs
Based on the itinerary as listed, you'll make good savings with a 7 day JR Pass . If you use my recommendations above, this may change to something like:
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Kansai airport > Kyoto: ¥3,690 (75mins, 99km)
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Kyoto > Uno: ¥8,780 (130mins, 252km)
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Uno > Kyoto: ¥8,580 (139mins, 252km)
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Kyoto > Kanazawa: ¥6,910 (124mins, 224km)
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Kanazawa > Odawara: ¥15,950 (294mins, 544km)
JR ticket cost: ¥43,910 for 5 legs
As you can see you'll have slightly less savings with the recommended route, but will be spending less time on trains.
You can look up precise train timetables and costs at the Hyperdia travel planning website and learn how to use Hyperdia for JR Pass holders through our video blog.
Hope this helps!