Heat the oil in a medium saucepan over high heat. Add the onions and cook until soft. Add the garlic and cook for 1 minute. Add the wine and cook until reduced by half.
Add the tomatoes, water, ancho, chipotle, pasilla, honey and cook over medium-high heat until the sauce has thickened, stirring occasionally, about 20 to 30 minutes. Season with salt and pepper and stir in the lime juice just before removing from the heat.
Heat 2 inches of oil in a medium skillet over medium heat until it reaches 350 degrees F on a deep-fry thermometer.
Fry tortillas, one at a time, until crisp, 20 to 30 seconds. Drain on paper towels and season immediately with salt.
Heat a large nonstick skillet over high heat.
Add the chorizo and cook until golden brown. Remove with a slotted spoon to a plate lined with paper towels and let cool slightly. Remove all but 1 tablespoon of the rendered fat. Add the butter to the pan; when the butter melts, turn the heat to down to medium.
Carefully crack the eggs into the pan, season with salt and pepper, and cook, until the whites are completely firm but the yolks are still soft, about 2 minutes.
Combine the crema and lime zest in a small bowl. Place a few spoonfuls of the red chile sauce on four plates. Place a fried tortilla on top of the sauce. Divide the eggs over the tortillas and ladle the warm tomato-red chile sauce over. Sprinkle each with about 3 tablespoons of the cheese and some of the lime crema and garnish with the crisp chorizo and chopped cilantro. Serve immediately.