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 the chile paste.
Sprinkle the chuck roast with salt and pepper and then dust the chuck roast with flour.
Turn the oven to 275 degrees F. Heat oil in the Dutch oven over medium-high heat. Once the oil is hot, add the chuck roast and brown on one side, about four to five minutes. Carefully flip the chuck roast and brown on the other side. Remove the chuck roast from the Dutch oven and set aside.
Reduce heat to medium. Add the onion and jalapeños to the pot. Cook until softened, about four to five minutes. Add the garlic and cook for 30 seconds, stirring constantly.
Pour in remaining 4 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. Place the chuck roast back in the Dutch oven.
Bring the heat back to medium-high and boil the mixture. Once it boils, cover and place in the oven. Cook until the beef easily shreds with a fork, about three hours.
Remove the chili from the oven. Carefully remove the chuck roast and place it on a cutting board and give it a few minutes to cool. Meanwhile, place the pot of chili back on the stove and turn the heat to medium to simmer. Whisk together the cornstarch and water to make a slurry. Stir in the cornstarch slurry with the beans and let it simmer for about 10 minutes until it thickens.
As the chili simmers, use two forks to shred the chuck roast. Discard any pieces of fat. Stir the shredded beef into the chili. Serve with your favorite toppings. Enjoy!