Fry bacon in a large skillet until crisp, remove to paper towels to drain. Add panko bread crumbs and toast in skillet until golden. Remove from heat and crumble bacon into bread crumbs, toss to combine.
Using salted water, cook the pasta according to package directions, but do not rinse; set aside.
Melt butter in a large saucepan over medium-low heat; whisk in flour until smooth. Continue whisking and cook for 2 minutes. Gradually whisk in the milk. Whisking constantly, cook for 5 minutes or until thickened. Reduce heat to low and stir in salt, black pepper and most of the cheese (note: add cheese about a cup at a time, stirring to incorporate so as not to cause graininess).
In a large bowl combine cooked pasta and cheese sauce. The sauce will be thin, but will thicken once baked.
Pour the pasta mixture into a lightly greased 8 x 11 x 2 baking dish. (Use a spatula to scrape out every ounce of that saucy goodness.) Sprinkle the top with the remaining cup of cheese and sprinkle with the prepared bacon/panko topping. (note: a layer of shredded parmesan cheese may be added prior to the sprinkling of the crumb topping, if desired.).
Bake at 400° for 20-30 minutes or until bubbly. Remove from oven and allow to rest about 10-15 minutes.