I own a 50ES but from what I heard 50ES remotes seem not to use exactly the same IR code as 9000ES'. I was using a ccf file delivered by Paul Shen who has teached a lot of codes from the sony remote (50ES as well). Adding more I didn't have any problems with the functions buttons. The direct access DSP mode buttons made some trouble first. But I've found a way to learn them all, though the code might not be super-clean I'm happy with them as they do work perfectly.
There's a thread about the 9000ES remote at
www.prontoedit.com in the programming forum.
Phil