Heat oven broiler. Place garlic, tomatoes, chiles, and quartered onion on a foil-lined baking sheet; broil, turning as needed, until lightly charred, about 8 minutes for garlic and 12 minutes for the tomatoes, chiles, and onion. Let cool slightly, then peel garlic, tomatoes, and chiles; transfer vegetables to a blender and set aside.
Place 12" skillet over high heat; add pasillas. Cook, flipping once, until lightly toasted, about 2 minutes. Transfer to a bowl and cover with 3 cups boiling water; let sit until soft, about 20 minutes. Drain chiles, reserving 1 cup soaking liquid; remove stems and seeds from chiles. Transfer chiles and soaking liquid to blender; add stock, tomato paste, and cumin. Purée until smooth; pour through a fine-mesh strainer into skillet; boil. Reduce heat to medium; cook, stirring occasionally, until thickened, about 20 minutes. Stir in lime juice, salt, and pepper; transfer sauce to a shallow bowl.
Wipe skillet clean and add 3 tbsp. oil; heat over medium-high heat. Cook minced onion until soft, about 5 minutes; transfer to a bowl. Add remaining oil to skillet; heat over medium-high heat. Working in batches, fry tortillas until pliable, 10–20 seconds. Transfer to a plate; let cool slightly.
Heat oven to 375°. Pour 1 cup enchilada sauce in the bottom of a 9" x 13" baking dish; set aside. Dip tortillas in remaining enchilada sauce; divide onions evenly among tortillas and top each with 2 tbsp. cheddar. Roll tortillas tightly around onions and cheese. Arrange tortilla rolls seam side down in prepared dish. Pour remaining sauce over rolls, and cover evenly with remaining cheddar and Monterey Jack cheeses; bake until cheese is melted and sauce is bubbly, 18–20 minutes. Garnish with scallions, cilantro sprigs, and sour cream; serve with refried beans and rice if you like.