Heat oven to 350. Lightly spray baking dish with cooking spray, I use a 1-2 qt. oval one, but you can use square too.
Cook pasta as directed and drain, set aside.
Dice peppers and onion, cook and cut into 1 inch cubes, toss together and set aside in a bowl.
In a large sauce pan, melt butter over medium heat. Stir in flour, cook until it starts to turn a light golden brown color. Gradually stir in broth. Heat to boiling, stirring constantly; remove from heat.
Stir in milk, cumin, chili powder, cayenne pepper and salt. Add Monterrey Jack cheese and stir until melted, remove from heat.
Add in vegetables and chicken, green chiles, then add in pasta. Stir until well combined.
Pour into prepared pan, cover, and bake in oven until pasta is warm and bubbly, about 15-20 minutes.
Remove from oven and serve. Top with Cotija cheese and fresh pico.