In a medium bowl, whisk together all marinade ingredients: soy sauce, miso paste, mirin, brown sugar, sesame oil, garlic, ginger, and pepper. It will form a thick, viscous paste.

Place chicken thighs in a large zip-top bag or shallow dish. Pour the thick, gooey marinade over the chicken and massage to coat every piece.

Marinate in the refrigerator for at least 30 minutes, or up to 24 hours for best results.

Preheat oven to 400°F (200°C). Line a 9x13 inch baking dish with parchment paper (do not skip this step).

Arrange the chicken thighs in a single layer in the prepared dish. Scrape any remaining marinade from the bag and spoon it over the chicken.

Bake for 20 minutes. Remove from oven and baste the chicken with the pan juices. Return to oven and bake for another 15-20 minutes, until cooked through (165°F / 74°C).

Turn the oven broiler on high. Place the dish under the broiler for 2-5 minutes, watching closely until the glaze is bubbly and caramelized in spots.

Remove from oven and let the chicken rest in the pan for 5-10 minutes. The thick, gooey glaze will thicken as it cools. Serve hot.