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1
Bring 1/2 cup of the water to a boil.
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2
Put the chiles in a bowl and pour the boiling water over them.
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3
Let the chiles soak until softened, about 20 minutes.
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4
Reserve the soaking liquid.
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5
Stem and seed the chiles.
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6
In a blender, puree the chiles, quartered onion, garlic, tomatoes, oregano and thyme with the vinegar and 2 1/2 teaspoons of the salt.
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7
Combine the flour with the remaining 1/4 teaspoon salt and the pepper.
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8
Dredge the beef in the flour.
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9
Shake off the excess.
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10
Reserve 3 tablespoons of the dredging flour.
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11
In a large pot, heat the oil over moderately high heat.
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12
Add about a third of the meat.
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13
Brown well on all sides, about 8 minutes, and remove.
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14
Brown the remaining beef in two more batches, adding more oil if needed.
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15
Remove.
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16
Reduce the heat to moderately low.
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17
Add the chopped onions and cook, stirring occasionally, until soft, about 5 minutes.
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18
Add the reserved flour and cook, stirring, for 1 to 2 minutes.
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19
Raise the heat to moderately high.
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20
Add the chile puree and cook, scraping the bottom of the pot, for 3 minutes longer.
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21
Return the beef to the pot with any accumulated juice.
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22
Add the reserved chile-soaking liquid and the remaining 4 cups water and bring to a simmer over moderately high heat.
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23
Reduce the heat and cook at a bare simmer, partially covered, for 1 hour and 20 minutes.
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24
Add the squash and bell peppers and cook, partially covered, until the meat and vegetables are tender, about 25 minutes longer.
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25
Serve with lime wedges, if you like.
