I also followed the Futaba FAQ's and it worked for me. I had to change things slightly though.....I have a Y-harness connecting my flaps (only thing I can't do is Full-Span ailerons). I keep meaning to change this, but keep forgetting about it.
If you're looking to get a book, get the newer one out by Anne Marie Cross. She actually wrote the 9C manual that comes with the radio.