To roast the jalapeno - set the oven broiler to high. Place the jalapeno on the top wrack. Keep a close eye, and turn the pepper to lightly char on all sides. For a spicier sauce, include the whole pepper instead of half in the cheese sauce. For less spice, remove the pith and seeds.
While the pasta is cooking, combine everything under “Cheese Sauce” in a blender and blend to combine. Melt the butter in a medium saucepan over medium high heat. Stir in the all purpose flour and continue stirring for 1 minute. Slowly whisk in the cheese sauce from the blender, a little at a time to fully incorporate into the flour. When the sauce begins to boil, remove from heat and stir in the cheddar shreds. Stir until the cheese is mostly or fully melted.