Make the dashi: Combine the water and kombu in a small saucepan and soak 20–30 minutes. Heat over medium until small bubbles appear around the edges (do not boil), then remove the kombu. Add the katsuobushi, turn off the heat, and steep 2–3 minutes. Strain through a fine sieve; you should have about 2.5 cups.
Prepare the fillings: Cut the chicken thigh into 0.5-inch cubes. Peel and devein the shrimp (halve if large). Thinly slice the shiitake mushrooms and the kamaboko. Rinse the ginkgo nuts.
Make the custard base: In a bowl, lightly beat the eggs just until homogenous, avoiding bubbles. Measure 2.5 cups (600 ml) of the warm dashi and let it cool to lukewarm, then stir in the usukuchi soy sauce, mirin, and kosher salt. Slowly whisk the seasoned dashi into the eggs. Strain the mixture through a fine sieve into a pitcher to remove bubbles and chalazae.
Assemble: Divide the chicken, shrimp, shiitake, kamaboko, and ginkgo nuts among 6 small heatproof cups (5–6 oz/150–180 ml). Pour the egg mixture gently into each cup, leaving a little headspace. Cover each cup tightly with a lid or foil to prevent water droplets from entering.
Steam: Set up a steamer over gently simmering water (barely bubbling). Place the covered cups in the steamer, reduce heat to low, and steam until the custard is set at the edges and softly jiggly in the center, 12–15 minutes for small cups. A skewer inserted should release clear broth with no liquid egg.
Finish and serve: Turn off the heat and let the cups rest, covered, 5 minutes. Uncover and top each custard with a few mitsuba leaves (for serving). Serve hot or warm.