Try resetting your PRAM and NVRAM first, as this cured a few cases of dead FireWire ports on the old G4 Cubes... if that doesn't work, then resetting the motherboard via the PMU reset switch may help.
The PMU reset switch is on the motherboard, and, I believe, labeled "S1" and located somewhere around the battery. Power down and remove the power cord from your computer (and all cords connected to the computer). Open the case, and look for a small switch on the motherboard labeled "S1" or close to the battery, and press it for about 1/2 second: click, stop. Do not press the switch more than once, as doing so may fry the PMU (once is safe, though). Wait at least 10 seconds, then connect everything back up and power on.
