Hi,
My wife and I were about to travel to Japan on the above itineraries coming December. We are going to depart from Airport (either Haneda/Narita) upon touching down earlier in the morning.
May I know if the above itineraries work with JR Pass? Also, we probably will stay one night in Osaka, two night in Kyoto, two nights in Mount Fuji and 3 nights in Tokyo. Can someone advice if 9 days will be good enough? Thanks.
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http://www.japan-guide.com/e/e5200.html
http://www.japan-guide.com/e/e6900.html
The former is far more convenient to get to with regards to your plans though, and there are good regional passes you can get for the area:
http://www.odakyu.jp/english/deels/
The Hakone Loop course covers the whole Hakone area in a day, and it has some good hot springs (onsen) to visit, which you should do at least once in your stay.
When you arrive at the airport matters also - if too early, the office to get your pass won't be open. You can see the official list at:
http://www.japanrailpass.net/en/exchange.html
If you arrive at Narita, it is easy to get the Narita Express into Tokyo, and if Haneda, you can take the monorail in.
It's unclear what you mean by "good enough". Will you see all the best sights in Japan? Of course not - you could spend a couple months in Kyoto and not see it all.
Since you are already seeing Tokyo, you can largely skip Osaka during the day. After the temples of Kyoto close down around 5 PM, you can zip over to Osaka for the evening. At night the city comes alive and has some great places to see, such as Dotonbori, plus the night views from the Umeda Sky Bldg, and Abeno Harukas Bldg are wonderful. Instead, take that time and go see Nara, which is also one of the crown jewels of traditional Japan and has some of Japan's most unforgettable sights.
Personally, unless you have your heart set on spending 2 full days by Fuji, I'd take one of them and use it to go see Hiroshima/Miyajima as a full day trip, or go see Himeji (with Japan's finest castle). You would rack up huge savings using the rail pass for this, and both are excellent places to visit.
You can see regular fares, routes and schedules on Hyperdia
http://www.hyperdia.com
Since you are using a 7 day rail pass for a 9 day trip, if you are leaving Japan from Narita, the cheapest way back is the 1000 yen bus:
http://accessnarita.jp/en/home/
A 3 day subway day pass can save you some money too:
http://www.tokyometro.jp/en/ticket/value/travel/index.html#anc03
Good luck.