I'm not sure when the last time it was that I tried this (As in, why shutdown at all? I can currently find out how long it has been since I moved my computer from one desk to another by typing "uptime" in the terminal), but when I did try it, all it took was booting into OS 9 once. When booted in 9, set the startup time in the Energy control panel, and then set your OS X drive as your startup disk in the Startup Disk control panel.
-Bruce Adcock