Over medium-high heat in a large Dutch oven or stock pot, toast the dried chiles until fragrant, about two to three minutes. Add 2 cups beef stock and bring the mixture to a simmer. Cover, reduce heat and continue to simmer for 10-15 minutes until the chiles soften and are pliable.
Add the chiles and beef stock used to simmer the chiles to a blender with the chipotle peppers and adobo sauce. Blend until smooth. Set aside.
Sprinkle salt and pepper all over the short ribs. Lightly dust with flour. Add oil to the large Dutch oven or stock pot over medium-high heat. Once the oil is hot, add half the short ribs and brown on all sides, about two to three minutes per side. Remove and reserve on a plate. Repeat with the second half of short ribs and remove and reserve on a plate.
Reduce the heat to medium. Add the onion and jalapenos to the pot. Cook until softened, about four to five minutes. Add the garlic and cook for 30 seconds, stirring constantly. Pour in remaining 3 cups of beef stock, strong coffee and reserved chile paste, scraping up the bottom of the pot with a wooden spoon.
Stir in the diced tomatoes, tomato paste, apple cider vinegar, cocoa powder, brown sugar and spices. Add the short ribs back to the pot. Bring the heat back to medium-high and boil the mixture. Once it boils, reduce the heat to a simmer. Put the top on, leaving a small crack open. Simmer until the short ribs can be easily removed from the bone, about two and a half to three hours.
Remove the short ribs from the Dutch oven and add the drained beans to the pot and cover. Give the short ribs a few minutes to cool. When the short ribs are cool enough to handle, shred the meat off the bone. Stir the shredded short ribs back in the pot. Serve with your favorite toppings. Enjoy!