Heat smoker to 225 degrees F. As it heats, sprinkle the chuck roast with salt and pepper on both sides.
Place the chuck roast in the smoker with a water pan. Insert a leave-in digital meat thermometer in the center of the roast. Close the lid and smoke until the chuck roast reaches an internal temperature of 155-165 degrees F, about three and a half to four hours.
While the chuck roast smokes, you can take care of the chili base. Over medium-high heat in a large Dutch oven on the stove, 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.
Heat oil in the Dutch oven over medium heat. Once the oil is hot, 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. Turn off heat and reserve until the chuck roast is ready.
When the chuck roast finishes smoking, let it rest for 10 minutes. After resting, turn up the heat on the smoker to 275 degrees F. As the smoker comes up to heat, cut the chuck roast into bite-size cubes and discard any pieces of fat. Add the chuck roast to the chili with the beans. Turn the heat on the stove to medium-high and bring the chili to a boil.
Remove the chili from the stove and place on the smoker uncovered. Close the lid on the smoker and let the chili smoke for another two to three hours. Stir occasionally. Serve with desired toppings. Enjoy!