Preheat an oven to 325 F.
Prep and sear the beef. Cut the beef into 2-3 inch cubes and season all over with salt and pepper. Heat the oil in a 5 qt dutch oven over medium heat. Once the oil is hot and shimmering, add the beef in a single layer to the pot and brown on all sides--you may need to do this in batches. Transfer to the beef to a plate.
Saute the onions. After searing all the beef, add the onions to the pot and cook for 3-4 minutes. Add the garlic and spices and cook for another minute. Stir in the minced chipotle peppers and fire roasted tomatoes and bring to a simmer. Add in the broth and bay leaves and bring to a simmer.
Braise the beef in the oven. Add the beef back to the pot and season the broth with salt and pepper. Stir well and cover. Transfer to the oven and braise for 3-3 1/2 hours, until the beef is tender and easily shredded. Let the beef rest in the juices for 20 minutes before shredding and seasoning to taste with salt and pepper.
Prep the bowl ingredients. Add the oil to a skillet over medium heat and saute the sliced peppers and onion until softened. Stir in the cilantro and lime to the rice and season to taste.
Assemble the bowls. Add cilantro-lime rice to a bowl and top with the shredded beef, peppers & onions, and black beans. Top as desired with salsa, guacamole, and shredded lettuce.