Preheat the oven to 350 degrees . In a large skillet, cook the bacon over medium heat, stirring frequently, until crisp, about 8 minutes. Using a slotted spoon, transfer to a paper-towel-lined plate. Pour off all but 1 tbsp. fat, add the apples and cook, stirring frequently, until browned and beginning to soften, about 5 minutes. Transfer to a bowl.
Place the leeks in a colander in the sink. In a pot of boiling, salted water, cook the pasta until al dente, 4 to 5 minutes; drain in the colander with the leeks to soften them.
In a medium saucepan, melt the butter over medium heat. Add the flour and cook, whisking constantly, for 1 minute. Whisk in the milk; cook until smooth and thickened, about 10 minutes. Remove from the heat and add 1 1/2 cups cheese and a generous sprinkling of pepper; whisk until smooth.
In a bowl, add the pasta and leeks, the sauce, apples and parsley; toss well. Reserve 1/4 cup of the bacon. Add the remaining bacon to the pasta; toss. Season with salt and pepper.
Divide the pasta among four 16-oz. baking dishes, top with the remaining 1/2 cup cheese, cover with foil and bake for 30 minutes. Sprinkle with the reserved bacon and serve hot.