Place the livers in a bowl and add the milk to cover. Cover the bowl with plastic wrap and refrigerate for at least 8 hours or overnight. Drain well and pat livers dry.
In a large skillet cook the bacon over medium-high heat until crisp and all of the fat is rendered, 4 to 6 minutes. Remove the bacon and transfer to paper towels to drain. Set bacon aside. Reserve the bacon drippings. Add the livers and cook, stirring occasionally, for 3 minutes. Add the shallots, garlic, thyme, 1 1/2 teaspoons of the salt, and the pepper and cook until the livers are just slightly pink and the shallots are soft, about 1 to 2 minutes longer. Add the cognac and cook until the liquid has evaporated and the livers are cooked through but still tender, 2 to 3 minutes. Transfer to a large shallow bowl to cool.
Once cooled, place the liver mixture together with any drippings in the bowl of a food processor and add the cream cheese and 1/2 pound butter and process until smooth. Add salt to taste if necessary.
Spoon the mixture into small ramekins or serving bowls and smooth the tops with a rubber spatula. Cover tightly with plastic wrap and refrigerate until firm, 4 to 6 hours.
While the mousse is chilling, melt the remaining 2 tablespoons of butter over medium heat in a large skillet and add the onions. Season with the remaining 1/4 teaspoon salt and the sugar and cook, stirring occasionally, until the onions are very soft and caramelized, about 20 minutes. If the onions begin to toughen or get too dark around the edges before they are soft and caramelized, add a bit of water, as necessary. Season the onions with salt and pepper, to taste, transfer to a small bowl and set aside until ready to serve the mousse.
Crumble the crisp-cooked bacon into a small bowl.
To serve the mousse, place the ramekins on a plate and serve with the toasted croutons. The caramelized onions and crumbled bacon should be nearby in small bowls for guests to garnish their mousse-spread croutons. (Alternatively, spread the mousse on the croutons and garnish with the onions and crumbled bacon and pass the assembled hors d'oeuvres on a platter.)