Well! The service source PDF I had consulted was the October 11, 2004 version. I found an updated version (March 11, 2005) which has changed the pictures and description on page 16 to match the RAID card manual. At least now I can sleep in peace on that matter.
However, I think the two FireWire 800 ports on the back of the XServe are dead. I have tried resetting the PMU (CUDA button) and PRAM, Open Firmware (reset-nvram, set-defaults & reset-all), starting in Safe Mode, and have tried a known good drive using known good cables in a known good external casing which has USB, FW400 and FW800 ports. This external drive shows up when connected via USB, FW400 (into the FW400 port on the front), and also from the hard drive's FW800 port via a FW800 to FW400 adapter cable going into the front FW400 port on the XServe. The only way it does not show up is via a FW800 cable from the drive's FW800 port to either of the FW800 ports on the back of the XServe.
I think I have covered most of the usual troubleshooting options. Is there anything I can try in Terminal? Might there be a connector (for the FW800 ports) somewhere inside the XServe which could have become unplugged sometime in the past (before I acquired it)? System Profiler shows the FireWire Bus as having a maximum speed of 800 Mb/sec, but it also show "Unknown Device" even when nothing is plugged into any of the FireWire ports. Disk Utility shows nothing. I have also tried booting from an internal drive with OS X Server (10.4.11) installed, just in case there was something in the "normal" version of the OS software that might be affecting things. I observed no difference.
I can live without FW800 but it would be nice to have it available if possible. Does anyone have any ideas on other hardware or software approaches to try? It's not worth replacing the logic board (if that's what is required) - I may as well put that cost toward something more up to date. Is there any diagnostic software, similar to the hardware test disc's for eMac's and other models, which will work on an XServe? I have had a brief look at the XServe Remote Diagnostics, and it is very technical (command line stuff, NetBoot, extra computer needed, etc.) compared with booting from a CD/DVD.