For the sauce: Bring the mirin to a boil in a saucepan. Add soy sauce, water and bonito flakes and bring to boil again. Reduce heat and simmer for about 2 minutes. Remove from heat, strain and let it cool to room temperature. You can refrigerate until serving time or up to 24 hours, then use as a dipping sauce.
For the soba: Boil the soba according to the directions on the package. Stir occasionally to keep from sticking. To check for doneness, pinch a noodle strand between your fingers. They should be tender yet slightly firm to the bite. Rinse well in cold water and drain.
Divide the well-drained soba among 4 zaru (bamboo) or lacquer or pottery plates. Garnish nori threads over the top.
Place a 1-teaspoon mound of wasabi, grated daikon radish and a neat pile of green onions on a small dish. Fill small, deep, cup-size bowls halfway with chilled dipping sauce. Serve all the dishes together. Serves 4