Coat a large saucepan with olive oil. Toss in the onion, season with salt and bring to medium heat. Cook the onion until soft and very aromatic, 8 to 10 minutes. Toss in the garlic, jalapeno and chorizo and cook for 3 to 4 minutes more, breaking up the meat with a spoon.
Add the chopped cilantro, chipotles, adobo sauce and tomatoes. Season with salt, taste and season again if needed. Stir in 1 cup water, increase the heat to high, bring to a boil and reduce the heat to a simmer. Cook for 30 to 35 minutes, or until the mixture has a good saucy consistency. Taste and adjust the seasoning if necessary.
While the sauce cooks, fill a large saucepan with about 3 inches of canola oil. Heat the oil over medium-high heat to about 375 degrees F (or add a slice of tortilla to the oil -- when it sizzles, starts to float and crisps up, it's ready). While the oil heats up, put a couple of paper towels on a baking sheet next to the stove. When the oil is hot, work in batches to fry the tortillas until they are crispy chips. Remove the chips from the oil, drain on the paper towels and sprinkle with salt.
Preheat the oven to 350 degrees F. In a large bowl, toss a third of the chips with a third each of the tomato sauce and cheeses. Spread the chip mixture in the bottom of a large ovenproof casserole dish, then top with another third of the chips, sauce and cheeses. Repeat the process with the remaining chips, sauce and cheeses. Bake for 15 minutes, or until the cheese is melted.
When the casserole comes out of the oven, coat a large saute pan lightly with olive oil. Add the eggs (you will probably have to work in batches to fry all of them -- no worries) and bring the pan to medium heat. Cook the eggs until the whites are cooked through and the yolks are warm and runny, about 4 minutes. Place the fried eggs on top of the chips. Sprinkle with the whole cilantro leaves. Serve with the lime wedges and crema.