Place the beef chuck roast in the slow cooker. Add the minced chipotle peppers, garlic, sliced yellow onion, beef broth, lime juice, cumin, oregano, salt, and black pepper. Stir the liquid around the meat to distribute the seasonings.
Cover and cook on low for 8 to 10 hours until the beef shreds easily with two forks. The broth keeps the meat moist throughout the long cook time.
While the beef cooks, combine the sliced red onion, apple cider vinegar, sugar, water, and a pinch of salt in a bowl. Stir well and let it sit at room temperature to pickle.
Once the beef is done, shred it directly in the slow cooker and mix it with the juices. Warm the corn tortillas.
Fill each tortilla with shredded beef, a spoonful of pickled onions, and a sprinkle of chopped cilantro.