In a large skillet over medium heat, add ground beef and season with salt and freshly ground black pepper. Break down the meat while cooking until half way done. Add red onions and sauté until soft and translucent, about 4 minutes. Transfer to a colander to drain then return meat mixture back to skillet.
Add chipotle purée, garlic, green chilies, taco seasoning and oregano. Stir ingredients very well before removing from the heat. Preheat oven to 400ºF.
To assemble the nachos, cover bottom of a deep dish pizza pan with tortilla chips. Spoon half beef mixture on top followed with ¼ cup red peppers, half can sliced black olives and sprinkle 1 cup each of Monterey Jack and Cheddar cheese. Repeat with the second layer starting with tortilla chips, remaining beef mixture, remaining ¼ cup red peppers and the rest of black olives. Add about 15 pickled jalapeño peppers and cover with the remaining 2 cups of cheeses. Add more jalapeño pepper (about 15 more).
Transfer dish to preheated oven and bake for 7 minutes or until cheeses are melted and ingredients are heated through. Remove from the heat and garnish with diced tomato and sliced green onions. Serve with salsa, guacamole, refried beans and sour cream. Serve 4 to 6.