I love this story. The plotline and the characters are /excellent/. Your characterization of Fratley made me like the character, your Amarant is fantastic and true to canon, and Gudrun is so well-characterized and introduced that it feels like she's a natural part of the canon FF9 world. Your older Puck seems like a natural progression of his character as well.
Your other original Burmecian characters rock as well, especially Sigurd. Someday he'll learn what an inside voice is. Maybe.