Well, I managed to get it to work, though I can't say I really fully understand just WHY it works. All I did was stop monitoring all IRQ's in the BIOS, then turn on ACPI in the kernel. I didn't compile any of the modules with it. Just the ACPI support part. (IE, no ac adapter, battery, fan, etc) and it seems to work. I have all USB devices working AND the system powers down when I halt it. Since it's a desktop that's all I really need.
I'd like to learn more about ACPI and how Linux interacts with it. It seem to be a kind of voodoo to me right now.
Time to head over to the tldp and read the ACPI howto.