Toast & Prepare Spices: In a small dry pan over medium heat, toast cumin seeds, shaking often, until fragrant, about 90 seconds. Grind to a powder. Combine with chili powder, smoked paprika, marjoram, and chipotle.
Sear the Beef: Pat beef dry. Heat oil in a large Dutch oven over medium-high. Sear in two batches until well browned on all sides, 5 to 7 minutes per batch. Transfer to a plate.
Build the Aromatic Base: Reduce heat to medium. Add onions and red bell pepper, scraping up browned bits, and cook 6 to 8 minutes until softened. Stir in garlic, jalapeños, pasilla strips, and the spice blend. Cook 60 seconds, stirring constantly.
Deglaze and Simmer: Pour in stout, scrape the pot, and reduce by about half, 5 to 7 minutes. Stir in crushed tomatoes, diced tomatoes, 2 1⁄2 cups broth, chocolate, maple syrup, bay leaves, salt, and black pepper. Return beef and juices.
Slow-Simmer the Stew: Bring to a gentle bubble, reduce heat to low, cover, and simmer 1 1⁄2 to 2 hours, stirring occasionally, until beef is fork tender and the liquid lightly coats the back of a spoon.
Incorporate Final Ingredients: Stir in beans and roasted red peppers. Return to a simmer and cook uncovered 20 to 25 minutes to thicken and meld flavors.
Finish and Serve: Turn off heat. Remove bay leaves. Stir in parsley and lime juice. Let rest 10 minutes. Skim any visible fat and ladle into bowls. Top with optional garnishes if desired.