In a large saucepan, combine the meat with 4 cups water. Bring to a boil, then reduce the heat and simmer for 15 minutes. Skim the froth, then cover and simmer for 1 hour and 15 minutes.
Meanwhile, in a small saucepan, combine the chiles with 1 cup water. Bring to a boil, then simmer for 15 minutes. Let cool.
In a blender, process the chiles and their liquid until you have a smooth sauce, about 1 minute. Pass the sauce through a strainer, and reserve ½ cup of the liquid.
To the meat in the saucepan, add the onion, tomato, and bell pepper. Stir in the ½ cup chile liquid, tomato sauce, Holy Trinity, oregano, bay leaves, and salt.
Simmer for 20 minutes.
Meanwhile, heat the oil in a small skillet over medium heat. Whisk in the flour and stir until golden in color. Remove from heat and add a small amount of liquid from the stew pot and stir to remove any lumps.
When the meat is tender, whisk in the flour mixture. Stir occasionally while simmering for about an hour, or until the stew is thickened. Serve immediately.
Notes
*In a spice grinder, combine 3 peeled garlic cloves, 1½ teaspoons cumin seeds, and 1¼ teaspoons peppercorns, along with 1 tablespoon water. Process into a smooth paste.