Bike Camping in Japan- on a shoestring
.. probably provides an extreme example.
Japan Youth Hostels, Inc.
probably provides a better example of affordable accomodations for students. And backpacking hotels like the New Koyo
at Y2500 per night are about as cheap as you can get.
Cheap 'traditional' "Japanese fast food" shops like Yoshinoya
are ubiquitous with their beef bowl
still priced at Y280. Not exactly healthy but at least you have a benchmark to work from.