How to Make It
Bring 1/2 cup of the water to a boil. Put the chiles in a bowl and pour the boiling water over them. Let the chiles soak until softened, about 20 minutes. Reserve the soaking liquid. Stem and seed the chiles. In a blender, puree the chiles, quartered onion, garlic, tomatoes, oregano and thyme with the vinegar and 2 1/2 teaspoons of the salt.
Combine the flour with the remaining 1/4 teaspoon salt and the pepper. Dredge the beef in the flour. Shake off the excess. Reserve 3 tablespoons of the dredging flour.
In a large pot, heat the oil over moderately high heat. Add about a third of the meat. Brown well on all sides, about 8 minutes, and remove. Brown the remaining beef in two more batches, adding more oil if needed. Remove.
Reduce the heat to moderately low. Add the chopped onions and cook, stirring occasionally, until soft, about 5 minutes. Add the reserved flour and cook, stirring, for 1 to 2 minutes. Raise the heat to moderately high. Add the chile puree and cook, scraping the bottom of the pot, for 3 minutes longer.
Return the beef to the pot with any accumulated juice. Add the reserved chile-soaking liquid and the remaining 4 cups water and bring to a simmer over moderately high heat. Reduce the heat and cook at a bare simmer, partially covered, for 1 hour and 20 minutes. Add the squash and bell peppers and cook, partially covered, until the meat and vegetables are tender, about 25 minutes longer. Serve with lime wedges, if you like.