Cook linguini according to package directions. Drain and keep warm.
In a skillet, cook onion or shallots and garlic in butter, stirring constantly until tender, not brown. Stir in sour cream, 2 tablespoons Parmesan, milk, lemon-pepper, salt, lemon juice and lemon zest. Cook for about 1 to 2 minutes. Remove from heat and pour over linguini. Toss gently, adding chopped parsley, chives, and remaining Parmesan. Serve warm.