In a large pot, cook the bacon over medium heat until the fat is rendered and the meat beginning to crisp, about 8 minutes. Using a slotted spoon, remove the bacon from the pot and reserve.
Add one-third of the garlic and the lemon juice to the bacon drippings and cook until the garlic is fragrant, 2 to 3 minutes. Add the quahogs, 2 1/2 cups water and the wine and bring to a simmer. Cover the pot and steam the clams until they open, about 10 minutes. Remove the clams from the pot. Strain the broth and reserve. Take the clams from their shells, chop them and set aside.
Meanwhile, melt the butter in a large saucepot over a medium flame. Add the onion, celery, remaining garlic, and chorizo and cook until the onion is translucent, 4 to 5 minutes. Stir the flour into the pot. Cook the onion and flour mixture for several minutes then add the clam broth and bring to a simmer, stirring until smooth. Add the tomatoes and sugar, stir well to incorporate, then toss in the pepper flakes, thyme, and parsley. Season with sea salt and freshly ground black pepper. Cover and cook at a low simmer until the broth is flavorful, 20 to 30 minutes.
Ten minutes before serving, add the littleneck clams and bacon to the soup. Cover and steam until the clams open, about 8 minutes. Add the reserved chopped clams. Stir well, season again, if needed, with sea salt and freshly ground black pepper, and serve immediately.