Hi there!
For your second week, I think I'll recommend the following:
- Immediately travel to Kyoto (or get your return flight back to Osaka Kansai)
- 3 nights Kyoto. Day trips to Osaka, Hiroshima and Nara (cut if needed)
- 1 night Hakone/fuji
- 2 nights Tokyo + Flight home (day trip to Nikko World Heritage Site)
This way you'll maximise your time experiencing the country. For this trip, a Nationwide JR Pass would be the only pass that would give coverage to your travel. Lets take a look at your costs assuming you fly down to Osaka from Sapporo and work your way back up the country.
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Kansai airport > Kyoto: ¥3,690 (75mins, 99km)
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Kyoto > Nara: ¥690 (44mins, 41km)
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Nara > Kyoto: ¥690 (44mins, 41km)
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Kyoto > Osaka: ¥540 (28mins, 42km)
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Osaka > Kyoto: ¥540 (29mins, 42km)
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Kyoto > Hiroshima: ¥10,990 (112mins, 380km)
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Hiroshima > Kyoto: ¥10,990 (126mins, 380km)
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Kyoto > Odawara: ¥11,950 (177mins, 429km)
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Odawara > Tokyo: ¥1,450 (36mins, 83km)
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Tokyo > Nikko: ¥5,630 (121mins, 150km)
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Nikko > Tokyo: ¥5,630 (117mins, 150km)
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Tokyo > Narita airport terminal 1: ¥3,140 (58mins, 79km)
JR ticket cost: ¥55,930 for 12 legs
Note that if you do not do a day trip to Hiroshima or Nikko it may not be worth getting a 7 day pass (except for the total flexibility). Also note that for Hakone the JR Pass gets you as far as Odawara. From here you'll need to use the non-JR Odakyu lines up to Hakone itself. I recommend the 2 day Hakone Free Pass for this, which can be purchased on arrival at Odawara.
Hope this helps!
