For everything you need to know about travelling Japan, see The Japan National Tourist Organisation’s (JNTO’s) website http://www.jnto.go.jp/eng/
There is a wealth of information about many places to visit, with details how to travel there, budget and other accommodation, transport and cultural tips. Also check out http://www.youtube.com/visitjapan to see all the famous people and tourists visiting Japan since the earthquake and Tsunami. Please check the map of Japan http://www.jnto.go.jp/eng/location/maps/index.html to see where the cities and tourist attractions are located. Click on the particular city that you are interested in and a summary will appear with a link to detailed page and tourist. For example, click on Hiroshima and then click on Miyajima. Then at the bottom of the Miyajima pop up, page click on Detailed page and information on the tourist attractions at Miyajima will appear as follows: http://www.jnto.go.jp/eng/location/regional/hiroshima/miyajima.html
JNTO- Accommodation Search http://www.jnto.go.jp/eng/arrange/accomodations/This is an excellent site and you can check out budget accommodation , Youth Hostels and Japanese inns, plus more expensive accommmodation.
Budget Accommodation across Japan http://www.seekjapan.jp/budget-accommodation Great site with budget accommodation across Japan.
Japan Youth Hostels http://www.jyh.or.jp/english/
one night around Y 2,500 - Y4,000 per bed
(share room, bunk beds, tatami mat rooms, singles, doubles, family room - around Y5,000) can be a little noisy at times, most with a curfew time at night, and country hostels are usually quieter than city ones.
Toyoko Inn chain http://www.toyoko-inn.com/e_hotel/00078/index.html has economical priced hotellocated around Japan. Prices range from Y7,400 single - Y9000 double in Tokyo and around Y5,500 single, $7500 double in country areas. These are comfortable business hotels, very clean and well run with free breakfast, TV, internet connection in room, computers in foyer and very easy to book Toyoko Inn hotels around Japan. Cleaning hotel from 10.00 AM. Become member for Y1500, stay 10 nights and get one night free, early check in, also discounts on first Monday and Sundays for members. Check out their web booking discounts.
Travel - Check out JNTO travel planner and lots of tips on traveling from the airports and around Japan. http://www.jnto.go.jp/eng/arrange/transportation/
Traveling in the Kansai Region - Kansai Pass
Cheap overnight busses http://willerexpress.com/bus/pc/3/top/;jsessionid=47EBAD121565E7A5E4543FAF18A9042F.ap34bus2
Happy Traveling and more tips to come on an E Book on How to travel Japan on a Budget - out soon on Amazon