Place the onion, jalapeño, and garlic in a pot and cover with water. Bring to a boil on high, then turn the heat down to low and simmer for 10 minutes or until softened.
Add the onion, jalapeño, and garlic to a blender, along with 1 cup of the cooking water. Also add to the blender the tomatoes, cumin, oregano, allspice, and cayenne, and blend until smooth.
Pour out the rest of the cooking water from the pot you cooked the vegetables, and add the oil and chorizo. While occasionally stirring, cook the chorizo on medium-low until fragrant and browned, about 10 minutes.
Pour the tomato salsa from the blender into the pot with chorizo, and while stirring occasionally, continue to cook until the salsa has darkened and slightly reduced, about 15 minutes. Squeeze in the lime juice then taste and adjust seasonings, adding salt to taste.
Meanwhile, while the sauce simmers, in a large heavy skillet heat 1/2 inch of oil on medium-high to 350°F, about 5 minutes. If you don’t have a thermometer, you can test the temperature by sticking a wooden spoon into the oil. If it bubbles around the spoon, it should be ready for frying. Line a large plate or sheet with paper towels.
Working in batches, add the quartered corn tortillas to the skillet and cook for 1 minute, turning once, until crisp. Remove with a slotted spatula and place on the lined plate. Continue until all the tortillas are fried. Lightly salt the fried tortillas.
For the chilaquiles, divide the fried tortillas onto 4 to 6 plates, and evenly pour over them the chorizo sauce. Top with diced onions, crumbled queso fresco, and cilantro leaves. Serve with guacamole on the side.