Adjust oven rack to lower middle position and preheat oven to 275°F Place chilis in bottom of a large Dutch oven and heat over high heat. Cook, turning chilis with tongs occasionally until fragrant and toasted, about 3 minutes. Cover with 2 cups chicken or beef stock. Bring to a boil over high heat, reduce to a simmer, and cook until chilis are completely tender, about 15 minutes. Remove from pot.
Rub kosher salt and pepper lightly on roast. Heat 2 tablespoons oil in now-empty Dutch oven over medium-high heat until shimmering. Sear chuck roast until well-browned on all sides, about 8 minutes total. Remove roast and set aside. Reduce heat to medium.
Add onions, cook 4 minutes. Add garlic and cook, stirring frequently, until fragrant (about 2 minutes). Add cumin, cloves, and oregano and cook, stirring constantly until fragrant, about 30 seconds. Add chipotle chilis and sauce, vinegar, and remaining chicken or beef stock. Scrape up browned bits from bottom of pan, simmer until reduced by about half, then transfer entire contents to the jar of a blender (or use stick blender).
Add soaked chilis and their liquid to the blender/pot. Start blender on low and slowly increase speed to high. Puree until smooth, about 1 minute. Set aside.
Place beef chuck in Dutch oven. Add bay leaves and bring to a boil over high heat. Place lid on pot slightly cracked, then transfer to oven. Cook, turning beef occasionally, until completely tender, about 5 hours. Discard bay leaves and transfer chuck to a large plate. Return Dutch oven to stovetop and cook, stirring frequently, over medium-high heat until liquid is reduced to about 1 1/2 cups, about 5 minutes.
Shred beef into large chunks with fingers or two forks. Return beef to a pot along with the sauce. Bring to a simmer and cook, gently stirring and folding until beef is hot, tender, and coated in sauce. Season to taste with salt. Serve immediately, piling the beef into warm corn tortillas with onions, cilantro, salsa, limes, or other condiments as desired.