Firewire 800 Problems

try the following;

1. Shut-down your Mac, and unplug the power cord
2. Turn the power off on your external FireWire devices
3. Unplug the FireWire devices from the Mac
4. Wait for 5 min.
5. Plug the power cord to your Mac only
6. Restart the Mac while holding the Option-Apple-O-F, and keep holding until you get the ">" prompt, then release the keys
7. At the ">" prompt type:
reset-nvram and hit the Return key
set-defaults and hit the Return key
reset-all and hit the Return key
the last command will restart your mac
8. Shut down your Mac
9. Connect all your FireWire devices to the Mac and turn them on
10. Restart your Mac.

All your FireWire devices should reapear, if not repeat the procedure

How to avoid the issue :
The only really proven way to avoid burning up a FireWire port is to connect all devices and to turn them on PRIOR turning on the Mac. Likely, one must unplug them and turn them off AFTER the Mac has been turned off. If you need to connect another device, then you're on for a shutdown of your machine... 
It's a tad annoying but it guarantees that the FW ports won't be damaged. 
Be careful when using self powered devices such as webcams, iPods, hard drives or hubs, as they can destroy the port pretty easily. Another thing is to avoid daisy-chaining hard drives.

When the FW port doesn't respond anymore :
In this case, peripherals won't be mounted upon plugging, and won't be displayed in Apple's System Profiler. The self powered devices will still be fed by the port, but won't respond either. 
It happens that the PHY just hangs after a surge or a random problem. Once hung, the port will not respond any longer, it is possible to reset the component by going through the following steps :
1° boot the mac in Open Firmware by holding [ Apple key - Option - O - F ] after the startup chime. 
2° you'll get to a command prompt. the keyboard mapping will be QWERTY, so pay attention when you type the following : 
RESET-NVRAM (enter) 
RESET-ALL (enter) 
3° Now the mac should restart itself and the port should function properly again. 
If it still doesn't work, then it means that the PHY is damaged.

http://www.hardmac.com/articles/16/