Pat beef cubes dry with paper towels and season generously with 1 teaspoon salt and black pepper.
Heat bacon fat in a large Dutch oven over high heat. Working in batches, sear beef cubes on all sides until deeply browned, about 8-10 minutes total per batch. Transfer to a plate.
Reduce heat to medium and add chopped onion to the pot. Cook until softened, about 5 minutes, scraping up any browned bits from the bottom.
Add minced garlic and cook for 1 minute. Push onion mixture to the side and add ancho chili powder, chipotle pepper, cumin, garlic powder, and oregano to the cleared space. Toast spices in the beef fat for 30 seconds until fragrant, then stir into the onions.
Stir in tomato paste and cook for 2 minutes until it darkens slightly.
Return beef and any accumulated juices to the pot. Add beef broth and coffee, stirring to combine. Bring to a boil.
Reduce heat to low, cover partially, and simmer for 2.5 hours until beef is fork-tender, stirring occasionally.
Mix masa harina with 3 tablespoons water to create a smooth paste. Stir into the chili along with honey, remaining salt, and apple cider vinegar. Simmer uncovered for 15 minutes to thicken. Serve with lime wedges for squeezing over the top.