Preheat oven to 350˚F. Prick potatoes all over with a fork and place directly onto center oven rack, 2 inches apart. Bake potatoes until fork tender, 1 hour to 1 hour 15 minutes.
Remove potatoes from oven and cool until no longer steaming. Peel potatoes and dice.
Place a large pot over medium heat and melt butter. Add shallots and saute for 2 to 3 minutes. Season with salt and pepper.
Add flour and continue to cook for 3 to 4 minutes.
Stir in milk and stock until no lumps remain and continue to simmer until mixture thickens enough to coat the back of a wooden spoon. Stir in potatoes, season with salt and pepper and simmer for 5 to 6 minutes.
Pour soup into a blender, blend soup until smooth, about 2 minutes.
Pour soup back into pot and stir in sour cream and adjust seasonings. (If soup is too thick, stir in an extra ½ cup to cup of milk).
Ladle soup into bowls and top with a bunch of shredded cheese, crumbled bacon, sliced chives, and crispy shallots or onions, if using. Finish with more cracked black pepper and serve.
