Once you de-flood Faron Woods, go to Skyloft and speak with Owlan. He is on the top floor of the Knight Academy, in his room. Agree to help him finish up his plant collection and head to the Faron Woods, landing at the “Viewing Platform” Bird Statue.
Now, go southeast from there, towards where Oolo the Kikwi is (you can find that on your map). Speak with Oolo and bring Scrapper in to carry Oolo. Go speak with Instructor Owlan for your five Gratitude Crystals.