Heat a large cast iron skillet over medium-high. Arrange whole tomatoes, onions (cut-side down), and garlic in the dry skillet in a single layer. Cook, turning occasionally, until charred on all sides, about 6 minutes for garlic and 12 minutes for onions and tomatoes.

Transfer charred vegetables to a blender and add chipotle peppers. Process until smooth, about 1 minute.

Stir salt, chili powder, cumin, and black pepper together in a small bowl. Season beef evenly with salt mixture.

Heat oil in a Dutch oven over medium-high heat. Add beef in batches and cook, turning occasionally, until browned on all sides, about 3 minutes per side. Transfer browned beef to a plate.

Pour water into the Dutch oven and scrape up any browned bits from the bottom. Stir in onion-tomato mixture, brown sugar, oregano, and bay leaves. Reduce heat to medium-low and bring to a simmer.

Nestle beef back into the pot, cover, and cook, stirring occasionally, until beef is tender and shreds easily with a fork, 1 hour 45 minutes to 2 hours 15 minutes. Remove bay leaves and discard.

Remove beef from the pot, shred using two forks. Return shredded beef to the pot, stir in lime juice to combine.