Short version:
We have a hard drive in the RAID on the server that was failing. It's always the simplest things in the end, but at first it really looked like something gone haywire with journaling on the drives, or mysql going bonkers, or something similar.
We've since taken the bad drive out of the RAID, and spent the last 24 hours or so backing up several hundred gigs of data off-server as a precaution. I've had the forum offline during this time.
We still have more to look at, and need to get the bad drive replaced, so there will be additional downtime in the near future.
Also, while we suspect the RAID was the alpha and omega of the problems, only time will tell if other issues need attention. The server seems responsive enough right now, but I'm still seeing occasional spikes of high CPU usage with corresponding server lag, so I'm not holding my breath just yet.
More updates when I have them. Thanks!
--- saint