To make the chipotle taco meat, in a large skillet, heat the oil over medium-low heat. Add the beef and onion and cook, stirring occasionally, until the beef is lightly browned and the onion is translucent, about 10 minutes.
Add the garlic and cook for 30 seconds more. Add the tomato, chili powder, cumin, oregano, cayenne, chipotle chile, salt and black pepper. Stir until the spices are well distributed, turn down the heat, and simmer for 15 minutes, stirring occasionally. Stir in the masa harina until well combined, then taste and adjust the seasonings, if needed. Stir in the lime juice and remove from the heat.
To make the nachos, pour 1⁄2 inch of oil into a heavy skillet and heat to 350°F. If you don’t have a candy thermometer, after 5 minutes of heating, you can stick a wooden spoon into the oil to see if it’s ready. If the oil bubbles around the spoon, it should be hot enough. In batches, fry the tortillas for 1 minute, until golden brown, turning once. drain on a paper towel and sprinkle lightly with salt.
Place the chips close together but not overlapping on a baking sheet or large cast-iron skillet, and top each with 1 teaspoon refried beans, 2 tablespoons chipotle taco meat, and 2 tablespoons cheddar cheese.
Bake for 5 minutes, or until the cheese is melted. After removing the nachos from the oven, top each with 1 tablespoon guacamole, 1 tablespoon sour cream, and 1 pickled jalapeño slice. Serve warm, with salsa on the side.