1. Preheat the oven to 400ºF. Spray a large baking dish with nonstick spray.
2. Bring a large pot of salted water to a boil. Add the pasta and cook until it is al dente, about 10 minutes. Drain and set aside.
3. Meanwhile, in a large soup pot, melt the butter over medium-high heat. Add the bell peppers, chili pepper and bacon and cook until the peppers soften, about 4 minutes. Add the scallions and cook 1 minute more.
4. Stir in the adobo sauce, flour, chili powder and cumin and cook for 1 minute.
5. Gradually whisk in the milk and simmer until the sauce thickens, about 5 minutes. Remove from heat. Stir in 3/4 cup of each cheese and cilantro. Stir in the cooked pasta and chicken.
6. Spoon the pasta mixture into the prepared baking dish. Sprinkle the remaining cheese over the top. Bake until the cheese is melted and bubbly, about 10 to 15 minutes.
(This can be prepared in advance and stored unbaked in the refrigerator for up to 2 days.)