One of the great things about staying in Japanese minshuku and ryokan (besides the bath!) is that the price of the room includes both dinner on the night you check in and breakfast the next morning. Of course it goes without saying that these will only be Japanese meals. Little or no "western" food will be available. If you stay in a hotel, though, typically no meals are included and you will be on your own to go out and find something.
A Typical Minshuku Dinner
A Typical Minshuku Breakfast
For lunch each day, you can eat at restaurants or buy food at grocery stores and convenience stores along the road and make your own. Most restaurants have a set price lunch that is reasonably cheap, especially if you like ramen and tonkatsu. Grocery stores and convenience stores almost always have ready made sandwiches of various kinds for as little as a few hundred yen. However, from time to time there will be long stretches of road where you won't see a restaurant or store all day. When you are in rural areas like this, always be sure to carry some crackers, bread, or the like, in your pack as an emergency lunch. Choose something that will keep so you can eat it on another day if you do suddenly stumble on a restaurant.
If you always want to make your own lunch, there are plenty of grocery stores as Japan is the land of mom and pop stores and convenience shops. In the rural areas, you may not always find much, but you should be able to buy enough to put together a respectable lunch. I very rarely eat in restaurants, and usually eat sandwiches or bento (boxed lunch) that i buy at convenience stores. If i know i'm heading out into nowhere, i stop at a grocery store if i find one, buy some bread, a package of sliced ham, and a few rolls with bean paste inside. With a can of Aquarius or Pocari Sweat from a vending machine, this all makes a few great lunches.
The walker's guidebooks (Shikoku Henro Hitori Aruki Dōgyō Ninin by the Henro Michi Hozon Kyōryoku Kai, and Shikoku 88 Route Guide by Buyodo Publishing) list a lot of grocery stores and convenience stores in the rural areas to help you plan.