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; saut 4 minutes.
Add onions; saut 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.