Preheat oven to 375º F. Coat an 8×8 inch square baking dish with non-stick spray.
Prepare pasta according to package instructions and drain. Set aside.
Remove chorizo from casing and break up with wooden spoon in a skillet and brown over medium heat, about 5 minutes. Add onion, bell pepper and jalapeños (optional) and cook until just softened, about 3 to 4 minutes.
Sprinkle on flour and stir until well combined. Slowly stir in milk until combined, about 1 to 2 minutes. Whisk in both shredded cheeses and combine until you have a smooth sauce. Turn off heat.
Add cooked pasta to skillet and combine. Transfer mixture into the baking dish.
Add bread crumbs to the top of the casserole and bake for 20 to 25 minutes, or until bread crumbs are lightly browned and cheese is bubbly.
Remove from oven and let cool for 10 to 15 minutes before serving