@Indeva. I just came upon this thread. I also have a Biocube 32g for about one year now and am about to set up a fuge in the second chamber. I saw that you glued the side of the intake fuge rack with the sides of the factory medial tray.
How is this working for you? Did you have any issues with flow restriction. I read another thread where they removed the fuge rack and just kept the media rack and put the Chaeto in the open space. I think that may be a problem when removing the media tray.
Also can you send some pics of your light setup for the fuge in chamber 2?