Preheat oven to 400°.
Remove 1 teaspoon adobo sauce and 1 chile from canned chiles; mince the chile. Place remaining sauce and chiles in a zip-top plastic bag; freeze for another use.
Melt butter in a large Dutch oven over medium-high heat. Add bell pepper and bacon; sauté 4 minutes. Add onions; sauté 1 minute. Stir in the adobo sauce, minced chile, flour, chili powder, salt, and cumin; cook 1 minute. Gradually add milk; cook until thick and bubbly (about 4 minutes), stirring constantly with a whisk. Remove from heat. Gradually add 1 1/2 cups cheese and cilantro, stirring until cheese melts. Add pasta to pan; toss well.
Spoon the pasta mixture into an 11 x 7-inch baking dish coated with cooking spray. Sprinkle 1/2 cup cheese over pasta mixture. Bake at 400° for 15 minutes or until browned.