Messy Barbacoa Beef Nachos

Name: Messy Barbacoa Beef Nachos
Ingredients: 4 pound boneless beef chuck roast; kosher salt and coarse black pepper; 1 large red onion, peeled and thickly sliced; 8 garlic cloves, smashed; 2 ounce bittersweet chocolate; 1 (7.5 ounce) can chipotle in adobo, 2 chilies reserved; 3/4 cup brown sugar; 1 1/2 tablespoon dried mexican oregano; 1 tablespoon ground cumin; 1 teaspoon ground cinnamon; 1/2 teaspoon ground cloves; 3 bay leaves; 3 limes, halved; 1 (14.5 ounce) can reduced sodium chicken stock; 1 cup sour cream; 2 reserved chipotle chilies, finely chopped; zest and juice of 1 lime; 1 garlic clove, finely minced; 1 (16 ounce) bag sturdy lightly salted tortilla chips (i used el milagro brand); 1 cup queso quesadilla cheese; 1/2 cup shredded american cheese; 1/2 cup shredded sharp cheddar cheese; 3 cup barbacoa beef; 1 (15 ounces) can pink beans, rinsed and drained; 1 small white onion, minced; 1/2 cup chopped cilantro; cilantro lime cream; 4 scallions, snipped; 1 cup halved grape tomatoes; hot pickled nacho peppers (optional)