Prep the beef. Trim excess fat and cut the chuck roast into 3–4 large pieces. Pat dry and season all sides with salt and pepper.
Sear for flavor (optional but recommended). Heat oil in a large skillet over medium-high. Sear the beef on all sides until deeply browned, about 2–3 minutes per side.
Transfer to the slow cooker.
Build the sauce. In the same skillet, add onion and a pinch of salt. Cook 2–3 minutes until lightly softened. Stir in garlic for 30 seconds.
Add chipotles, adobo, cumin, oregano, cloves, and smoked paprika. Stir for 30–60 seconds until fragrant.
Deglaze. Pour in beef broth, lime juice, and apple cider vinegar. Scrape up browned bits.
Let it simmer 1 minute, then pour everything into the slow cooker over the beef. Add bay leaves.
Slow cook. Cover and cook on Low for 8–10 hours or High for 4–6 hours, until the meat shreds easily with a fork.
Shred and season. Remove bay leaves. Transfer beef to a board and shred with two forks.
Return to the slow cooker and toss with the juices. Taste and adjust with salt, extra lime juice, or a pinch of brown sugar if needed.
Reduce (optional). For a thicker sauce, ladle some cooking liquid into a saucepan and simmer 5–10 minutes, then pour back over the meat.
Serve. Pile into warm tortillas and top with cilantro, onion, and a squeeze of lime. Or spoon over rice with beans, grilled corn, and avocado for bowls.