A suggested rafting and hiking trip to Japan for me would involve the following:
1. Flying to Narita return can be expensive, so I offer an alternative of flying to another city, even Pusan, South Korea and catching a ferry to Fukuoka. At any Japan major city you can activate your 1 week Japan Rail Pass. As a side option, consider an overnight stay in Fukuoka, Nagoya, Hiroshima at a Capsule Hotel. These hotels are cheap (Y3000-4000) and you dont need to book. You can leave excess luggage (secured) in the office. You can take this opportunity to travel around each region by rail to see Japan, or spend the nights bar hopping in a foreign city. If you like drinking, go for the budget izakaya franchises like Hub (popular for expats).
2. Accommodation in capsule hotel in Tokyo: There are capsule hotels in the vicinity of the major stations like Ueno and Shinjuku. Shinjuku and Shibuya are best for drinkers. Capsule hotels tend to be targeted at Japanese people, so they have Japanese names. Nevertheless you can book a 'capsule' through a shinkansen (rapid train) station Tourist Information Office. Ask for the cheap options.
3. Book your train ticket to Minakami: Go to the Reservations Office in a major JR station and book a ticket to Minakami. There are various adventure companies operating from there whom can help you with your trip, or go to www.canyons.jp/index_E.html to make reservations. You can check the travel timetable at http://www.hyperdia.com/.
4. Next day go rafting at Minakami: If the adventure company does not pick you up from Joban Kogen Station, you will likely need to change trains at Takasaki or Numata.
5. Explore the options for mountaineering around Minakami, or if it is winter, you can travel through the range towards Niiagata, and there are several stations near the ski fields. Return to a capsule hotel in Tokyo.
6. Take your mountaineering day trip in Minakami or Matsumoto if you are looking for an alternative option. There are no budget capsule hotels in nearby Nagano unfortunately (http://wikitravel.org/en/Nagano), but there might be a budget ryokan (traditional guest house), or go a budget busines hotel for Y5000-6000. Otherwise back to Tokyo.
7. Narita City: On your last day you might want to stay at Narita City so you dont have to far to go the next day for your flight. I suggest staying at the Central Hotel or Narita View Hotel, as they are cheap and are close to the station. There are alot of tourist places around Narita Station including bars, plus one of the best shrines in Japan. You can catch a train to the airport in the morning. Or get an express to Ueno-Fukuoka if you are flying out from Pusan with Korean or Asiatic Airlines.
Using a Korean Airline can make particular sense if you are flying on to other countries as JAL only allows you to stay in Japan on stopover for 12 days. Japan can be an expensive place to eat. The cheap options are franchise izakaya outlets in the major cities, as well as discount takeaway stores such as Hokka Hokka Tei (Best!) and Yoshinoya. See my blog posting about the Japan Rail Pass at http://the-rail-way.blogspot.com/.
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Andrew Sheldon www.sheldonthinks.com