Preheat oven to 375°F.
Cook noodles in a large pot of salted water until al dente, according to package instructions. Once noodles are cooked, drain and rinse with cold water.
Heat a medium saucepan over medium heat. Add butter and let melt completely. Once butter is melted, add flour. Whisk continually until flour is completely incorporated and cook until golden brown, about 2 minutes.
Add milk, whisking constantly. Continue to whisk until mixture comes to a boil and has thickened slightly, another 2-3 minutes.
Whisk in cheese until completely melted and smooth.
Remove from heat. Add pumpkin, nutmeg, and salt and stir until smooth.
Add noodles to the sauce, and stir until well coated. Add macaroni to a medium oven-safe dish.
Make the breadcrumb topping by combining pecans, breadcrumbs, butter, and a sprinkle of salt. Stir to combine, then sprinkle evenly over the macaroni.
Bake for 20-25 minutes, until the breadcrumb topping has browned slightly.