Preheat oven to 400˚F. 

Dry the short ribs on paper towels, and sprinkle with 1 teaspoon of the coarse salt and the black pepper. Heat 1 tablespoon of the oil in a large, ovenproof pot over medium-high heat. Working in batches, brown the ribs all over, and transfer to a bowl.

Place the kabocha squash on a rimmed baking sheet and toss to coat with the remaining oil. Roast 10-15 minutes, until caramelized (it doesn't need to be tender.) Remove from oven and lower the heat to 300˚F.

Add the onions and remaining teaspoon of salt to the pot you used for the ribs. Cook over medium-high heat about 3 minutes, until softened. Stir in the flour and cook, stirring, until deep golden brown, 4-5 minutes. Stir in the garlic and cocoa, and cook for 1 minute. Stir in the beef broth and brandy. Add the dried cranberries, ginger, and orange zest, and bring to a boil. Return the ribs to the pot, cover, and bake for 3 1/2 hours. Remove from oven and spoon off the fat. Fold in the kabocha squash and fresh cranberries, and return to the oven. Bake until the kabocha is tender, and the meat pulls away from the bone, about 30 minutes more.