To make Mole Sauce: Heat oil in large pot over medium heat. Add onions, and cook 10 to 12 minutes, stirring occasionally, or until browned. Stir in garlic, chili powder, brown sugar, cinnamon, ancho chili powder and ground cloves, and cook 1 minute, or until fragrant, stirring constantly.
Add tomatoes, cocoa, peanut butter and 2 cups water. Season with salt and pepper. Reduce heat to medium-low; cook 15 minutes, stirring occasionally.
To make Enchilalas: Preheat oven to 350F. Ladle 3/4 cup Mole Sauce into bottoms of 2 12x8-inch ovenproof baking dishes. Place about 2 1/2 tbs. cheese in center of each tortilla. Roll tortilla around cheese, and set seam side down on top of mole sauce, placing 8 filled tortillas in each pan. Top each dish with 1 1/4 cups mole, and sprinkle each with 1/3 cup cheese. Bake 20 minutes, or until sauce bubbles and cheese melts.