Toast & Prepare Spices: In a small, dry pan over medium heat, toast the whole cumin seeds, shaking the pan often, until fragrant (about 90 seconds). Immediately transfer to a spice grinder or mortar and pestle and grind to a powder. Combine the ground cumin in a small bowl with the salt-free chili powder, smoked paprika, marjoram, and chipotle powder.
Sear the Beef: Pat the beef cubes completely dry with paper towels. Heat the oil in a large Dutch oven over medium-high heat. Working in two batches, add the beef in a single layer and sear until a deep brown crust forms on all sides, about 5-7 minutes per batch. Transfer the seared beef to a plate and set aside.
Build the Aromatic Base: Reduce the heat to medium. Add the diced onions and red bell pepper to the pot, scraping up any browned bits from the bottom. Cook, stirring occasionally, until the vegetables soften and the onions are translucent, about 6-8 minutes. Stir in the minced garlic, diced jalapeños, pasilla chile strips, and the reserved spice blend. Cook for 60 seconds, stirring constantly, until the spices are highly aromatic.
Deglaze and Simmer: Pour in the stout beer, stirring vigorously to release all the flavorful bits from the bottom of the pot. Let it bubble and reduce by about half, which takes 5-7 minutes. Stir in the crushed tomatoes, diced tomatoes, unsalted beef broth, grated chocolate, maple syrup, bay leaves, the ½ teaspoon of salt, and black pepper. Return the seared beef and any accumulated juices to the pot.
Slow-Simmer the Stew: Bring the mixture to a gentle bubble, then reduce the heat to low, cover the pot, and maintain a very low simmer for 1.5 to 2 hours, stirring occasionally, until the beef is perfectly tender.
Incorporate Final Ingredients: Stir in the rinsed beans and the drained roasted red peppers. Increase the heat slightly to return to a simmer, then cook, uncovered, for an additional 20-25 minutes, allowing the flavors to meld and the stew to thicken.
Finish and Serve: Turn off the heat. Remove and discard the bay leaves. Stir in the fresh parsley and lime juice to brighten the flavors. Let the stew rest for 10 minutes before ladling into bowls. Top with optional garnishes if desired.