Preheat broiler. Bring a large pot of salted water to a boil. Cook pasta according to directions on the package. Drain and set aside.
While the pasta cooks, prepare the sauce. Add the bacon, if using, to a wide bottomed pot over medium heat. Cook until crisp — about 7 minutes. Remove the bacon, leaving behind any drippings, and drain on a paper towel.
Add the onion and garlic to the bacon grease and cook until softened — about 3 minutes. (If not using bacon, cook the onions and garlic in 1 Tablespoon of olive oil instead.) Add the jalapenos and cook for another 3 minutes. Stir in the flour. Cook for 1 minute, then add the vegetable stock. Simmer for 5 minutes.
Slowly stir in the Cheddar and Pepper Jack cheeses, adding a little at a time and letting it melt completely before adding more. Stir in the cream cheese. Mix in the crumbled bacon, if using.
Combine the cooked pasta and cheese in a shallow baking dish. Sprinkle a thin layer of bread crumbs over the top. Broil 3-5 minutes, or until bread crumb topping is crispy and golden brown.