Cut the chuck roast into large chunks and place them in the slow cooker. Add the chipotle peppers, garlic cloves, quartered yellow onion, beef broth, cumin, oregano, 1 teaspoon salt, bay leaves, and juice of 1 lime. Stir to combine the ingredients around the beef.
Cover and cook on low for 8 hours until the beef shreds easily with two forks. Remove the bay leaves and shred the meat directly in the slow cooker, then stir in the remaining lime juice.
While the beef cooks, make the pickled onions. Place the sliced red onion in a bowl with the apple cider vinegar, sugar, and 1/2 teaspoon salt. Stir and set aside to soften.
For the avocado crema, mash the avocados in a bowl until smooth. Stir in the sour cream, 1/2 teaspoon salt, and juice of the remaining lime until well combined.
Warm the corn tortillas. Fill each tortilla with shredded barbacoa beef, a spoonful of avocado crema, pickled onions, and fresh cilantro.