In a large pot over medium heat, bring kombu and 6 cups water to a simmer. Remove kombu as soon as the water starts to simmer or an instant-read thermometer registers 150º. Bring stock to a boil and add bonito flakes. Reduce heat to medium-low and bring to a simmer. Cook until stock is infused, 10 to 15 minutes. Strain through a fine-mesh sieve into a medium bowl, pressing on solids to release stock.
Return dashi to same pot and bring to a simmer over medium heat. Whisk in miso until dissolved, then stir in scallions and wakame.
Divide tofu among bowls. Pour soup over.
