Preheat the oven to 350°F. Butter a 2-1/2 -qt. baking dish. Bring a large pot of salted water to a boil; add the pasta and cook until al dente, about 6 minutes. Drain and set aside.
Meanwhile, melt the butter in a large saucepan over medium-high heat. Add the onion and cook until soft, about 3 minutes. Add the sausage, mustard powder, cayenne and 1 teaspoon salt and cook, stirring, until the sausage is golden, about 3 minutes. Stir in the flour and cook, stirring, until lightly toasted, about 2 minutes. Stir in the apple juice and cook, stirring occasionally, until thickened slightly, about 8 more minutes.
Slowly stir about three-quarters each of the Monterey jack and cheddar cheese into the sauce until smooth, about 2 minutes. Remove from the heat. Stir in the pasta and sour cream. Pour the mixture into the prepared baking dish. Sprinkle with the crushed crackers and the remaining cheese. Bake until bubbly, 25 to 30 minutes. Let rest 10 minutes before serving.