Elimination by gut region and function:
The gizzard and crop are both foregut structures concerned with food storage and mechanical grinding, they play no role in generating hindgut acidity. The midgut itself is typically alkaline, roughly pH 8 to 11, the opposite of what the question describes, so it can be ruled out as the cause.
The Malpighian tubules are excretory organs that empty their contents directly into the junction between the midgut and hindgut, they actively secrete potassium ions and nitrogenous waste, and this secretion lowers the pH of the fluid entering the hindgut, making it more acidic, roughly pH 4 to 6, as reabsorption of water and ions proceeds.
Having ruled out the gizzard, crop and midgut, the structure responsible for the hindgut's relative acidity is the Malpighian Tubules.