Heat oven to 350°. Place chiles in a large bowl, and cover with boiling water; let sit until chiles are soft, about 20 minutes. Drain, reserving 2½ cups soaking liquid, and then remove stems and seeds from chiles; transfer chiles to a blender along with reserved soaking liquid and garlic; puree until smooth, and set aside.
Heat 5 tbsp. oil in a 4-qt. saucepan over medium heat; add flour, and cook, whisking constantly, until mixture is a light caramel color, about 3 minutes. Add chile puree, vinegar, and oregano, and season with salt. Bring to a boil, and cook, stirring, until thickened, about 5 minutes; set chile sauce aside. Heat remaining oil in a 12" skillet over medium-high heat. Add onions, and cook, stirring, until golden brown, about 25 minutes.
To assemble, spread ¼ cup chile sauce in the bottom of a 9" × 13" baking dish. Dip one tortilla at a time into sauce, and then place on a plate; sprinkle with? cup cooked onions, ¼ cup cotija, and 1 tbsp. olives. Roll up tightly, and place in the baking dish, seam-side down; repeat with remaining tortillas, and more sauce, cheese, and olives.
Pour remaining sauce over enchiladas, and sprinkle with remaining cheese and olives; bake until heated through and cheese is just melted, about 40 minutes.