I just want to ensure that I'm not seeing anything abnormal here. Without any Firewire devices connected, what does your System Profiler show under the Firewire Device Tree? On my G5, all I have is one line: Firewire Bus; clicking it shows only one line of information, "Speed: 800Mb/sec Speed." The thing that piqued my curiosity is I noticed the USB Device Tree is populated with bus and device listings. Now, when I connected my iPod and refreshed Profiler, it listed the iPod under the Firewire Bus - I had admittedly expected a new Firewire Bus entry to pop up. Is it actually the case that all three G5 Firewire ports are on the same bus?
Interesting side-note trivia: If you haven't noticed it before, go take a look at the vendor name for the Apple Optical Mouse.