I think the budget guide is not too far off.
If you put more emphasis on the food, but less on the lodging (i.e., if you're OK to stay in a capsule hotel for example), it'll balance out.
You have such a range of choices of food in Japan, many of which are really good quality regardless of price. Cheap does not = bad in Japan if you do some research on where to dine.
When I was there, I ate at both high end and low end places but always ate very well. I think on average, for meals, you can spend $50USD per day; some days may cost only $20-25USD; others $100USD+ for a spectacular kaiseki dinner.
(Tip: go for lunches at the high-end sushi restos instead of dinner, and you'll still experience great food at a much more reasonable price.)