Cook the pasta according to the package directions and drain.
Heat the oven to 350 degrees. Spray mini muffin cups with nonstick cooking spray. Coat the cups with the bread crumbs and shake out the excess.
In a large saucepan, melt the butter over medium-low heat. Stir in the flour, jalapeno pepper, salt and chipotle chili. Cook and stir for 1 minute. Gradually stir in the milk and ½ cup sour cream. Cook and stir until thickened and bubbly. Remove from the heat. Gradually stir in the cheese just until melted and smooth. Stir in the cooked pasta and beaten egg until well mixed.
Spoon about 2 tablespoons into each muffin cup. Bake for 16 to 20 minutes or until dry around the edges and beginning to brown. Remove from the oven and let stand in the pan for 5 minutes. Carefully remove the cups to a serving plate. Garnish each cup with a small dollop of the remaining sour cream and sprinkling with the green onion.