Heat the water and kombu over low heat so it takes about 30 minutes to get close to boiling. Just before boiling, remove and discard the kombu, add the bonito flakes, bring the water to a boil, then simmer. Use a spoon to skim any foam that rises to the surface. Remove the water from the heat, wait for the bonito to sink to the bottom of the pan, then carefully ladle out the dashi broth, avoiding the bonito flakes as best you can. Strain the dashi through doubled cheesecloth, then cool, cover, and refrigerate until needed.