I have a G5 dual 2.3 that's sometimes experienced similar problems with USB. 
Mine were intermittent, and usually a Safe Boot reboot to clear the boot caches 
would clear the problem up. In my case, there were three USB ports available, 
one on the front, and two on the back. I noticed that usually only one port 
would have problems, like it was dead or something. I also noticed in System 
Profiler that the ports would often describe differently, sometimes identifying 
themselves as USB 1.1 ports (OHCI) and sometimes identifying themselves at USB 
2.0 ports (EHCI) "High Speed".

The keyboard & mouse I was using were both USB 2.0 compatible, and the keyboard 
had a "USB Hub" built-in, so I thought it was strange that the port would 
sometimes identify not as "High Speed" but rather as the older USB 1.1.

I never was able to sort out what the cause was. I did most of the same things 
you did, reset the PMU, PRAM, NVRAM, and I even looked at which USB extensions 
were loading. You can download developer versions of Apple USB extensions that 
create detailed logs of USB functionality. There are separate versions of these 
extensions for each OS version, so you'd need to get the ones for 10.5.8 
specifically. In my experience with unsupported OS X using xPostFacto I know 
that alternate versions of USB extensions (usually from earlier OS releases) 
often solve specific USB problems, but with a supported G5 using a supported OS 
version you'd think this generally would not be a good idea, other than perhaps 
using the developer version for 10.5.8 which I never did.

My only advise is try a Safe Boot from the external HD, and if the keyboard & 
mouse aren't recognized, try each of the three ports. You might also want to 
try a verbose boot using Cmd-v at startup to see if there are any USB error 
messages during the boot process?

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