Bring the vinegar, lime juice, miso, soy sauce, sugar, ketchup, yuzu kosho, garlic and ginger to a simmer in a medium saucepan over medium heat. Reduce the heat if necessary to keep at a low bubble for 20 minutes.
Remove the pan from the heat and stir in the bonito flakes. Steep for 5 to 10 minutes; the flakes will wilt and soften in the pan. If a smoother sauce is desired, blend or puree. Use immediately, or refrigerate in a nonreactive container for up to 2 days.