As you have mentioned on your post, department stores will be good place to check out for what typical middle class Japanese may eat.

Areas you have mentioned have department stores and will be easy to find. Usually at the top floor of department store is restaurants area. They are few restaurants to choose from, such as soba noodle restaurant, tempura restaurant, Chinese restaurant, Italian restaurant, etc. I mentioned department store restaurants because it is easy to locate, there are usually display outside of restaurants so you can see exactly what you are getting, and increases a chance that there is somebody who can speak basic English at restaurants.

Teishoku (定食) is a set meal usually comes on one tray. Rice, miso soup, main dish, and other small dishes such as pickled vegetable. Teishoku is what usually Japanese middle class salary men (サラリーマン) eats when they go out for lunch.

Obviously, restaurants at department stores may be little higher on price. Teishoku may be around JPY 1000 – 2000 and some may be higher.

If you go to small pop and mom type of teishoku-ya (定食屋), also popular by Japanese salary men, teishoku may start as low as JPY 500. Obviously at those places you can bet that nobody will speak English and menu is often written in Japanese only and often do not have those world famous plastic display of food. But you can bet it will be good old Japanese home type meal, close to what people may eat at home in Japan.