Place the beef chuck roast in the slow cooker. Add the diced onion, minced garlic, chopped chipotle peppers, cumin, oregano, salt, black pepper, beef broth, and lime juice.
Cover and cook on low for 8 hours until the beef is very tender and pulls apart easily.
While the beef cooks, prepare the pickled onions. Combine the sliced red onion, apple cider vinegar, sugar, water, and salt in a bowl. Stir well and set aside to pickle for at least 30 minutes.
Once the beef is done, shred it directly in the slow cooker using two forks. Stir the meat into the cooking juices to keep it moist.
Warm the corn tortillas. Fill each tortilla with shredded beef, top with pickled onions, chopped cilantro, and a squeeze of lime.