To prepare the marinade, preheat a heavy bottomed pan until very hot and add the sake. Bring to a boil to cook off the alcohol. Stir in mirin, sugar, miso and grated ginger and bring to a boil. Boil for approximately 10-15 minutes, cooking until it turns a pale caramel color. Remove from heat and allow to cool completely.
Cut the fish into 6 oz. pieces, leaving the skin on. Place the fish pieces in a pan and pour the marinade (reserving 1/4 of the marinade) over the fish until completely submerged. Allow to marinade for 3 hours to overnight. Heat oven to 375F. Wipe all excess marinade off the fillets and bake for about 45 minutes until lightly brown on top and the fish is cooked through. If pin bones are slightly sticking out, pull pin bones and discard. To finish, glaze fish with clean marinade and broil for an additional 10 minutes.