Make the waffle batter: Whisk together the buttermilk, eggs and honey in a small bowl. Whisk together the flour, cornmeal, baking powder, baking soda, cumin, fine sea salt and cayenne in a large bowl. Make a well in the center of the dry ingredients, add the wet ingredients and gently whisk together until just combined (do not over mix). Fold in the butter, cover the bowl with plastic wrap and refrigerate the batter for 30 minutes.
While the waffle batter rests, make the red chile sauce: Put the garlic on a cutting board, sprinkle with kosher salt, and use the flat side of your knife blade to smear the garlic and salt to a coarse paste. Heat the oil in a medium saucepan over medium-high heat. Add the onion and cook, stirring occasionally, until soft, about 4 minutes. Add the garlic and cook, stirring, until fragrant, about 1 minute. Stir in the tomatoes and their juices, the ancho and pasilla chile powders and some salt and pepper and bring to a boil. Reduce the heat to medium-low and simmer, uncovered, stirring occasionally, until the sauce is slightly reduced, about 15 minutes. Use a potato masher to mash the tomatos and cook slightly thickened, about 10 minutes longer. Mash again to make a chunky sauce. Stir in the chipotle puree, honey, vinegar and salt and pepper to taste, cook another 1 to 2 minutes then remove from the heat.
Make the crema: Combine the cilantro, garlic, cotija and pine nuts in a small food processor and puree the mixture until it is smooth. Whisk together the crema and goat cheese in a medium bowl until smooth. Stir in the cilantro mixture and lime zest and set aside. Season with salt and pepper.
Make the waffles: Heat the waffle iron according to manufacturer's instructions. Spray with nonstick pan spray, then ladle about 1/4 cup of the batter into each grid, close, and cook until golden brown on both sides and steam stops coming out from the iron, about 4 minutes. Transfer the waffles to a baking sheet.
Make the eggs: Preheat the broiler to high. Crack 4 eggs into each of 2 small bowls. Heat 2 medium nonstick skillets over medium-high heat (or use 1 skillet and cook the eggs in 2 batches). Add 2 tablespoons butter to each skillet; once the bubbles mostly subside, slip 4 eggs into each skillet and season the tops with salt and pepper. When the whites start to set, after 1 to 2 minutes, cover the skillet and cook until the whites are set and the yolks are still runny, about 2 minutes longer.
While the eggs cook, assemble the waffles: Combine the Cheddar and Moneterey Jack cheeses in a medium bowl, then top each waffle with about 1/2 cup of cheese and broil until the cheese is bubbly, 2 to 3 minutes. Top each waffle with a fried egg, a generous amount of chile sauce and a dollop of crema. Garnish with scallions and cilantro leaves and serve immediately.