Firstly, go to the Bazaar in Skyloft. At the restaurant place, speak with the big man there (he’ll have a speech bubble if this quest is active) and you’ll learn of rumors that there is a moaning in the Knight Academy restroom at night.
Go to the Knight Academy and speak with the old woman in the kitchen. She’ll also agree that there are some weird noises in the restroom (constipation? :P). Go in one of the rooms and sleep until nighttime.
Go to the restroom now and a voice will ask for some paper. You don’t have any paper yet, so just go into a bed and sleep until morning.
Now, go speak with Cawlin. He is in the hallway, near the restroom. He’ll ask you to deliver a love letter for him, specifically demanding that you don’t give it to the toilet-person. Anyhow, you’ll have two choices from here on out.
Option #1: Sleep until nighttime and go to the restroom. Hand over Cawlin’s love letter to the … thing to serve as … whatever it was meant to serve as. Sleep until morning and speak with Cawlin for a bit of a tantrum. Sleep until night once more and go into Groose’s room, Cawlin’s current residence, and speak with the disembodied hand haunting Cawlin for the five Gratitude Crystals.
Option #2: During the daytime, go to the first floor classroom and speak with Karane about the love letter. She’ll mention Pipit. Go up to the above floor and speak with him. Go back downstairs and speak with Karane. After the scene that occurs, you’ll receive five Gratitude Crystals.