Preheat oven to 350 degrees. Line a large baking sheet with aluminum foil, spray with non-stick cooking spray. Set aside
Heat a large skillet over medium heat. Add ground beef and onions; break up beef. Cook 3-4 minutes. Stir in chipotles, garlic, taco seasoning and beef stock. Bring to a low boil, reduce heat and simmer 6-8 minutes. Salt and pepper to taste.
At the same time heat a small sauce pan over medium low heat. Add pinto beans, honey, garlic & cumin. Simmer 5-6 minutes. Salt and pepper to taste.
Layer half of the tortilla chips on the baking sheet. Sprinkle ⅓ of the cheese over chips. Top with half of beef and beans. Layer remaining chips next, top with ⅓ of the cheese and remaining beef and beans. Sprinkle remaining cheese on top.
Bake 6-8 minutes until cheese melts. Remove from oven, squeeze limes over nachos and add desired toppings. Serve immediately.