1. Use a stand mixer to combine flour and 1 teaspoon of salt. Add in milk, eggs, and sour cream to form a shaggy dough. Cover and let it rest for an hour.
2. Meanwhile, boil the potatoes in a large pot of salted water until fork-tender, about 20 minutes. Drain and return them to the pot.
3. In a skillet over medium heat, caramelize the onions in butter until golden brown, about 20 minutes.
4. Mash the cooked potatoes with the caramelized onions, cottage cheese, cream cheese, bacon, cheddar cheese, and green onions. Season with salt and pepper.
5. Roll out the rested dough on a floured surface and cut into rounds. Spoon the potato mixture onto each round and fold in half, sealing edges by pressing firmly.
6. In a large pot, boil the pierogies in salted water until they float, about 4 minutes. Remove with a slotted spoon.
7. Serve the pierogies with additional butter, caramelized onions, and sour cream. Garnish with extra bacon, cheddar cheese, and green onions before serving.