In blender container, place sour cream, roasted red pepper, chipotle pepper, garlic, and salt, and blend until smooth.
Lightly grease waffle iron and preheat to high. Place 1 tortilla on waffle iron. Top with one-quarter of the chicken, cheese, tomato, onion, and cilantro. Place a second tortilla over filling, and close waffle iron. Cook until tortilla is golden brown, and cheese is melted, about 3 minutes, continuing to press down on waffle iron if needed during cooking to flatten further.
Remove quesadilla from waffle iron; repeat 3 times with remaining tortillas and stuffing ingredients. Cut into wedges and serve with pepper sauce and sliced avocado. Serve with lime wedges.