How old are you? If you are of 'student' age try and get an ISIC card, it might be handy when getting transportation. I managed to save about 4,000 yen off my ferry price with mine.
When I go to Japan in December Im only taking $500US or maybe a bit less, for about 4-5 days. Last time I went to Japan I only had about $120 for three days... depends if you're an extravagant spender or not. I could have quite happily spent hundreds more, but with my minimal funds I was not able to.
Food wise, it depends where you go, and how much you are willing to spend.
Luckily I didnt pay when I went to restaurants, I think I would have blown my budget in one sitting, but otherwise if you dont want fancy fine dining, but still good food at a reasonable price its definately out there.
Dont be too precious with the roadside 'caravans', they are great!
First you need to find out how much your airfare is roughly going to cost, get that out of the way, and just save as much as possible, when you run out of money you run out. So the more you can save the better a time you will have.
There are so many ways to cut down on prices of things.