Travelling in Japan

The best advice I can give you if you want to travel around Japan is not to live there. The Japanese government for years has been fighting the perception that their country is an expensive place to live and travel. As a result they have for many years been offering foreign tourists a very attractive concession pass for travel on Japan Rail's network. The Japan Rail pass is only available to foreigners travelling on a tourist visa, so my advice is finish any work visa before you travel around Japan. Thus if you are based in Japan, you are better off to see neighbouring countries. I would cancel your working visa so that you can freely travel back (from say Pusan or Seoul, Korea) with a Japan Rail pass & tourist visa. Its a requirement that you purchase the visa outside the country.
My strategy was to get a pass for 1 or two weeks and to travel as much as possible. I would planeach trip at night using www.hyperdia.com, trying to maximise the number of lines I could travel on, but always attempting to return to a large city by nightfall so I could find cheaper accommodation. In the larger cities (Tokyo, Hiroshima, Fukuoka) I knew I could find capsule hotels for Y3500-4500/night, often with a concession attached to the 2nd night. They obliged when I asked if I could store my large locked case in their backoffice.
In the smaller regional cities on the west coast I was having to mostly stay in business hotels, though they were not so bad at around Y4500-5000. Occasionally I would come across an inn which was cheaper. The trick is to make use of the shinkansen fast trains to get to remote outposts before you get local trains. If I left Tokyo on the first train I might expect to be in Fukushima by 8:30AM, so I can get a local train inland, maybe spending just one night in the mountains or on the west coast. I found that the train timetables in the alpine areas were not so helpful if you were transferring to another line. You need to plan the trip before you head inland. The staff were always very helpful telling me the connections. Sometimes (say around Miyoshi, near Okayama), a line might just have 2 or 3 trains a day. This poses a slight inconvenience since you can always take a different line as I often did. On occasion the train services in remote areas has been replaced by buses.
I have used a Japan Rail Pass 4 times now - the standard pass 3 times (7 & 14 day passes) and the 5-day flexible pass (gives you 5 days in a month) offered by JR East. Each has its merits. The standard pass suits people in Japan with a fixed agenda, the 5-day pass suits people who want to travel out on variable occasions, or who might want to use it on weekends.
For more info on the Japan Rail pass - see my Global Rail Travel blog.