OK, I've tracked down everything and fixed it. This may be useful information for others:
1. My "fried" onboard Firewire ports were fixed by resetting the PMU and doing an Open Firmware reset (see
this Apple Knowledge Base article or search the Apple support site for "pmu")
2. The firewire drive that wouldn't boot when connected to a PCI firewire card booted perfectly when connected to the built in firewire ports.
SuperDuper! had made a good copy/clone, I couldn't boot from it until I fixed the firewire ports.
Thanks for all the help.