Heat 1/4 cup of the oil in a medium pot over medium heat. Add the flour and whisk until smooth. Add the ancho chile, chipotle chile, cocoa, oregano, garlic powder and cumin and cook, whisking frequently, until the mixture is thickened slightly and fragrant, about 5 minutes. Add the chicken stock, whisk until smooth and continue to cook until slightly thickened, 2 to 3 minutes. Add the vinegar and season with salt and pepper.
Heat the remaining 1/2 cup oil over medium heat in a large skillet until shimmering. Quickly fry each tortilla in the oil, about 5 seconds per side; let drain on paper towels.
Preheat the oven to 375 degrees F.
Mix the Chihuahua, Cheddar and Monterey Jack cheese together in a bowl. Ladle about a 1/2 cup of the sauce on the bottom of a 9-by-14-inch glass baking dish. Stuff each tortilla with about 1/4 cup of the cheese blend. Roll the tortillas tightly and place seam-side down in the baking dish in 2 identical rows of 6. Cover with the remaining sauce and top with the remaining cheese.
Bake until the cheese is bubbly and golden brown, 10 to 15 minutes. Garnish with the pickled jalapeno and fresh cilantro.