Preheat the oven to 325°F.
Pat the chuck roast dry. In a small bowl, combine the cumin, smoked paprika, oregano, garlic powder, sea salt and black pepper. Season the beef generously on all sides.
Heat the oil in a large Dutch oven over medium-high heat. Add the chuck roast and sear for 3–4 minutes per side, until deeply browned. Transfer to a plate.
Reduce the heat to medium. Add the onion and cook for 3–4 minutes, stirring occasionally. Add the garlic and tomato paste and cook for another minute.
Add the orange juice, orange zest, lime juice and coconut aminos. Scrape up all the browned bits from the bottom of the Dutch oven.
Return the beef to the pot. Pour in 1½ cups beef bone broth and add the bay leaves. The liquid should come roughly halfway up the sides of the beef.
Cover and transfer to the oven. Braise for about 3 hours, or until the beef is very tender and easily pulls apart with a fork.
Transfer the beef to a cutting board and shred, discarding any large pieces of fat. Remove and discard the bay leaves.
Return the shredded beef to the Dutch oven and toss well with all of the concentrated braising juices. Add ¼ cup beef bone broth and toss again over low heat for 1–2 minutes, until the beef is juicy and well coated. If your Dutch oven still has plenty of braising liquid remaining, start with less broth and add only as needed.