In a large pot, combine the 5 cups water and kombu. Allow to sit for 30 minutes. After 30 minutes, bring to a boil over medium heat. Remove the kombu pieces and add another 2 tablespoons cold water. Stir in the bonito flakes until just combined. Once boiling, reduce to low heat and simmer for 5 minutes.
Skim off any foam that develops on the surface. Remove from heat and allow to sit for 15 minutes. Pour through a fine mesh strainer or cheesecloth into a large bowl. DO NOT squeeze the excess liquid from the bonito before discarding.
Return strained dashi (water cooked with kombu and bonito) to cleaned large pot over high heat. Stir in the usukuchi soy sauce, mirin, and salt. Once boiling, reduce heat to low until ready to serve.
To assemble the soup:
In a large pot, bring water to a boil over high heat. Reduce to a simmer and add the soba. Cook until just tender, about 4 minutes for dried soba and 2 for fresh. Drain, rinse in cold water, and divide among 2-4 bowls. Pour the hot broth over the noodles and top each bowl with desired toppings. Serve immediately.