Heat a heavy skillet over medium heat. Place dried guajillo chiles into the skillet and cook, turning occasionally, until the color changes and chiles have puffed, about 5 minutes. Set chiles aside to cool for a moment. Meanwhile, toast cumin and cloves in the hot skillet until cumin seeds begin to pop; remove from the pan and set aside. Remove and discard stems, seeds, and veins of chiles, and place into a small bowl. Pour boiling water over top, and cover. Let chiles soak for 1 hour.

Grind toasted cumin and cloves into a powder, and place into a blender. Add ancho chile powder, onion, garlic, oregano, thyme, vinegar, and lime juice. Remove chiles from soaking water, and place into the blender along with 1/3 cup of the soaking liquid. Cover, and blend until a smooth paste forms.

Place beef roast into a mixing bowl, and pour the guajillo chile paste over top. Coat beef on all sides with paste, then cover the bowl with plastic wrap. Marinate in the refrigerator overnight.

Preheat the oven to 325 degrees F (165 degrees C).

Transfer beef and marinade to a roasting pan, and arrange bay leaves over top. Cover tightly with aluminum foil. Bake in the preheated oven until beef is very tender and easily pulled apart with a fork, about 6 hours. Let stand, covered, at room temperature for 1 hour before discarding the bay leaves and shredding with two forks.