i want to spend 2 months in japan

im planning on going to japan for 1-2 months next year and would like to visit as much as possible this would mean probably 1 week maximum stays and a lot of travelling expenses, i was wondering what sort of rough budget i would need for this and what type of accomadation would best suit this?.
im planning on keeping to simple cheap food and would prefer to avoid big cities apart from a couple. any suggestions etc would be great thanks.

Some starting points:

Budget:
http://www.japan-guide.com/e/e2410.html

What to see:
http://www.japan-guide.com/e/e623a.html

General:
http://www.japan-guide.com/e/e623.html