Pat beef dry with paper towels; generously season with 1 teaspoon salt and black pepper.
Heat bacon fat in a large Dutch oven over high; sear beef deeply on all sides in batches, about 8-10 minutes total per batch. Transfer to a plate.
Reduce heat to medium; cook onion about 5 minutes until soft, scraping up browned bits.
Cook garlic 1 minute. Push onions aside; toast ancho powder, chipotle, cumin, garlic powder, and oregano in cleared beef fat 30 seconds until fragrant. Stir into onions.
Stir in paste; cook 2 minutes until slightly darkened.
Return beef and juices; stir in broth and coffee. Boil.
Reduce heat to low; partially cover and simmer 2.5 hours until fork-tender, stirring occasionally.
Mix masa harina with 3 tablespoons water into a smooth paste. Stir into chili with honey, remaining salt, and vinegar; simmer uncovered 15 minutes to thicken. Serve with lime wedges.