Preheat the oven to 475 degrees.
In a large pot of salted boiling water, cook the pasta for only 6 minutes, to be sure to keep it undercooked. Drain the pasta.
Heat a small skillet over medium heat and cook the bacon until the fat is rendered and the meat is crisp. When the bacon is cooked, drain it on a paper towel. Pour out all but 2 tablespoons of the bacon grease from the pan.
Place the chopped shallot in the pan and sauté at medium heat until they reach a deep brown; this should take about 10 to 15 minutes. Transfer the shallots, bacon, and pasta to a medium bowl and stir to combine.
In a large bowl whisk together the eggs and evaporated milk. Add the cayenne, nutmeg, salt, and cheeses. Stir to combine the ingredients. Add the par-boiled pasta to the spiced mixture and stir well. Transfer the bowl’s contents to an 8-inch square pan or 2-quart gratin dish. Even out the mixture and bake for 12 minutes until it is golden brown and bubbling. Let it sit for 10 minutes before serving.