Peel the onions and slice them thinly. In a large soup pot, combine onions, 1 cup of broth, oregano, cumin, salt, chile flakes and cayenne pepper. Cover and cook over medium high heat until most of the liquid has evaporated, about 25 minutes.
Uncover the pot and turn the heat up to high. Continue to cook the onions, stirring often and scraping any brown bits from the bottom of the pan, until the onions are well caramelized, about 15 to 20 minutes.
Meanwhile, combine the 6 remaining cups of stock with the flour and mix well to remove any lumps. Add the stock mixture to the onions and bring the soup to a boil.
Reduce heat and simmer the soup for another 15 minutes to blend the flavors, stirring often. Adjust the seasonings as needed.
Ladle soup into four bowls and top with shredded pepper jack cheese, fried tortilla strips, and cilantro or parsley, if desired.