In a small dry skillet over low heat add the ancho peppers, oregano, paprika, coriander, cumin, and chili powder. Cook until they begin to smell, about 2 minutes. Put the spices into a spice mill or food processor and grind until they are powdered. Set aside.
Heat a large heavy bottomed casserole over medium heat; add 3 tablespoons olive oil and the onions. Cook until the onions are soft and beginning to caramelize, about 10 minutes. Pat the beef dry and season it with salt and pepper. Add it to the pot and cook, stirring frequently, until it has browned on all sides, about 10 minutes. Add 2 tablespoons of the toasted spice mix, the garlic, chipotle, jalapeno, tomatoes, cinnamon stick, and sugar. Season with salt and stir well. Add some hot water until the meat is just covered with liquid. Return to the boil, reduce to a simmer, cover, and cook for 1 1/2 hours. Remove the meat and shred it with a fork. Return it to the pot, stir in the masa harina and chocolate, and cook for another 10 minutes, uncovered, to thicken. Taste and adjust seasoning. Serve with the queso fresco, cilantro, and lime for garnish.