Place guajillos in a large bowl, cover with boiling water, and weight with a small plate to keep submerged. Let sit until pliable, 15 minutes. Reserve 1 cup soaking liquid. Drain guajillos; discard stems and seeds. In a blender, blend guajillos, chipotle chile and sauce, and soaking liquid until smooth, about 2 minutes, scraping down side as needed. Pour mixture through a fine-mesh sieve set over a medium bowl, pressing on solids; discard solids. Set chile puree aside.
Heat a large Dutch oven or other heavy pot over medium-high. Season short ribs with salt and pepper and cook until browned, about 5 minutes. With a slotted spoon, transfer to a medium bowl. Add oil to pot, season beef chuck with salt and pepper, and cook until browned, about 5 minutes (do not crowd pot; work in batches if necessary). Transfer to bowl with short ribs.
Reduce heat to medium and add onion, garlic, and 1/2 cup water. Cook, stirring and scraping up browned bits with a wooden spoon, until onion is translucent, about 3 minutes. Add cumin, oregano, and cornmeal and cook until fragrant, 1 minute. Add meat, broth, chile puree, and just enough water to cover meat, if necessary; bring to a boil over high. Partially cover, reduce heat, and simmer 1 hour. Uncover and cook until meat is tender and chili is slightly thickened, 30 to 45 minutes. Add vinegar to taste.
Suggested toppings: corn chips, chopped white onion, grated cheddar, yellow mustard.
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