Preheat an oven to 400 F. Lightly grease a 9x13, or 3 quart baking dish with butter. Set aside.
Cook the pasta and prep the cheese. Bring a pot of salted water to a boil and cook the pasta to al dente. The pasta should still have some bite to it. This process is usually 2-3 minutes shy of the package instructions. Drain and rinse your pasta with cold water. If you do this step in advance, toss the pasta with a little oil to keep it from sticking. Use a box grater to shred the cheeses and set aside.
Render the bacon. Add the bacon to a 5 quart dutch oven over medium-low heat. Cook the bacon, stirring occasionally, until browned and crispy. Use a slotted spoon to transfer the bacon to a small bowl. Remove 1 tablespoon of the bacon fat and set aside.
Toast the sage breadcrumbs. Add 2 tablespoons of butter to the bacon fat left in the dutch oven over medium heat. Once the butter is melted and foamy, add 2 tablespoons of the chopped sage leaves and the panko breadcrumbs. Stir well and cook for 2-3 minutes, until the panko is toasty, but not browned. Transfer the panko to a small bowl and wipe out the dutch oven to remove any crumbs.
Build the cheese sauce. Add the reserved bacon fat and the rest of the butter to the dutch oven over medium heat. Once the butter is hot and foamy, add the shallots and remaining chopped sage. Cook for 3-4 minutes, until the shallots are soft. Stir in the flour really well and cook, stirring constantly, for 2-3 minutes to cook out any raw flour flavor. Switch to a whisk and slowly whisk in the half and half so that there are no lumps. Whisk in the pumpkin puree and bring to a gentle simmer, until thickened (about 5-6 minutes). Stir in the dijon, paprika, nutmeg, garlic powder, and heavy cream and let everything warm through for another 3-4 minutes. Remove the pot from the heat.
Add the cheese and pasta. Fold in the cheeses off the heat until completely melted. Season to taste with salt and pepper and add in ? of the cooked bacon and the cooked pasta. Stir well and then pour the mac and cheese into the prepared baking dish.
Bake. Top evenly with the sage breadcrumbs and remaining bacon. Cover with foil and bake for 15 minutes. Remove the foil and bake for 5-10 minutes more, until the cheese is bubbling and the topping is golden brown.