The Pedestals in Liquid Crystal
Complete all the puzzels in the Ruins of Alph in the order you wish, but Kabuto first (if you get: The puzzle has already been put into place. :go to a different one).
After they are completed then you are getting a message: Something has risen up on a distant island. :then the pedestales are there and then you are needing the red, blue and yellow flute. Speak with each of the pedestals and they will unlock the bird of there color. After that you will have lost your flutes and than you can searching the birds.
P.S.ost the locations of the birds here.