Cut the beef chuck roast (or beef cheeks if using) into 6 chunks and season all over with 1 tsp salt and ½ tsp black pepper. Heat a large skillet over medium high heat and add in olive oil. Sear beef on all sides until browned, about 3 to 4 minutes per side. Place seared beef in the bottom of a slow cooker.
Meanwhile, combine the beef broth, chipotle chili peppers, garlic and onion in the bowl of a food processor or blender and pulse several times to create a paste/thick sauce.
Add in brown sugar, cumin, oregano, remaining 1 tsp salt, and ground cloves and stir to combine. Pour over beef in slow cooker and add in 4 bay leaves.
Let beef cook on LOW heat for 8 hours. The beef should very easily fall apart. Remove the beef, shred with two forks. Stir the lime juice into the sauce in the slow cooker and return the beef. Cook an additional 20 to 30 minutes. Serve in tacos, burritos, enchiladas and more!