Rather than searching the web by using "cheap hotels Japan" or someother phrase, it is much handier to use one of the services like Rakuten or Yahoo! Japan to book your hotels. I have a Yahoo! Japan login, which I have used to book hotels online in Japan for the last 5 years. It works like a dream. You do not need a credit card.
There is a difference between 旅行 and 出張. Ryoko usually denotes pleasure and may well be ryokan or other weekend kinds of places. Shutcho are usually business hotels, and maybe accomodation only or the option to add meals.
The Japan Rail Pass is only available to "temporary visitors" (up to 90 days) and must be purchased outside of Japan and then activated once you are in Japan. They are sold as 7 day, 14 day, 21 day passes. You can buy several if you like and use them at different times.
There are also regional rail passes like the Kansai Thru Pass, which can be purchased in Japan and are 2 or 3 day passes.
You may NOT purchase or use a Japan Rail Pass if you have a student visa. Some students have used them before they start or after they have completed their study abroad by leaving the country to change visa status between student and tourist. South Korea is close and interesting.