Break up the Chorizo sausage into a large pan (remove casings if necessary). Add the ground beef and saute them together over medium high heat until nicely browned.
Drain the meat, reserving about 1 tablespoon of the drippings.
In the same pan, add the chopped onions, green pepper, jalapenos and garlic. Saute, stirring frequently, until the onions and peppers are limp, about five minutes.
Add the meat back into the pan along with the crushed tomatoes, diced tomatoes, jar of Alfredo sauce and the ground chipotle. Simmer for 30 minutes to an hour, depending on your own time constraints.
Preheat oven to 350 degrees.
Grease a 13x 9 inch pan (preferably a glass one... they don't leave off flavors like metal can with an acidic sauce)
Take the pasta you had already cooked and drained and add it to the sauce. Stir well (but gently) to combine.
Combine all the grated cheese. Add all of the cheese but 1 ½ cups to the pasta mixture. Stir well.
Pour into the prepared pan and smooth down. Top with the remaining cheese.
Put pan on on a cookie sheet (trust me on this... I could send you photos of my oven bottom as proof that you need to if you'd like :-P ) and bake casserole at 350 degrees until heated through, bubbly and cheese is melted, about 30 minutes.
Let rest for about ten minutes before cutting. Garnish with green onions and sour cream.