After the kombu has soaked overnight, bring the seaweed and its soak water into a medium-sized pot. Bring to a boil over a medium heat, then allow to simmer for 10 minutes. Add bonito flakes and remove from heat.
Allow soup to steep for another 10 minutes, then strain the broth into another pot. Bring to boil over a medium-low heat. Add tofu and cook for 1 minute. Remove from heat.
Ladle out about 1/2 cup of broth into a small bowl and mix in miso paste until it is completely dissolved and there are no lumps. Pour the miso into the rest of the broth and stir well. Place over medium heat just until the soup begins to simmer, then remove from heat and ladle into bowls. Top with sliced onion for garnish.
Nutritional analysis does not include onion for garnish.