In a large pot set over high heat, cover the short ribs with 1 inch of water; bring to a boil. Cook, using a spider skimmer to remove any foam that rises to the surface, for 10 minutes. Turn the heat to low, cover, and simmer until the meat is tender, 1½–2 hours. Remove from heat. Set a fine sieve over a large bowl and strain; set aside. Wipe out the pot and return it to the stove.
Meanwhile, in a large skillet set over medium-high heat, toast the bread, turning frequently, until lightly charred on both sides, about 5 minutes. Crumble into a bowl and set aside. Working in batches, char the tomatoes, tomatillos, onion, and garlic well on all sides, about 1 hour total, transferring the charred vegetables to a cutting board. Peel the onions and garlic and coarsely chop the vegetables. Remove the skillet from the heat. Add the cinnamon stick, pumpkin seeds, sesame seeds, and coriander seeds and cook, swirling the pan, until fragrant and lightly browned, about 2 minutes. Transfer to a blender.
In the blender with the spices, working in batches if necessary, purée the charred vegetables, bread,and guajillo and pasilla chiles, adding water a few tablespoons at a time as needed to make a thick sauce. (Refrigerated, the pepián will keep for up to 1 week.)
To the empty pot, add the oil and turn the heat to medium-high. When it is hot and shimmering, while stirring, carefully add the pepián all at once. Turn the heat to medium, then stir in the reserved beef and cook, stirring occasionally, until the sauce has thickened, 10–15 minutes.
Stir in the potatoes, chayotes, beans, salt, black pepper, and 2 cups of the reserved broth (save the remainder for other recipes). Bring to a boil, then turn the heat to medium-low and cover. Simmer until the vegetables are fork-tender, about 30 minutes. Ladle into bowls and serve.