Preheat the oven to 350°.
Grease a 13" X 9" X 2" pan.
Cook the sausage in a large skillet over medium heat, stirring frequently to crumble.
When the sausage is browned, add the onion, cumin, chipotle, garlic powder, black pepper, and salt and mix thoroughly. Cook until the onion is soft.
Remove the sausage from the heat and stir in the diced tomatoes and the sour cream.
In the prepared dish, layer half the macaroni. Then spoon on half the sausage mixture, covering the macaroni evenly. Spread half the cheese. Repeat this layering once more.
Whisk together the eggs and milk. Pour this mixture carefully over the casserole.
Cover the casserole tightly with foil and bake for 45 minutes.
Remove the foil and allow to bake an additional 15 minutes.
Remove from the oven and let rest for 10 minutes before serving.