more info:
OS X: after starting up the backup copy (250GB) on firewire, I moved it back to the ATA card, and it now starts up correctly there, as well!
OS 9: the backup copy still will not boot in OS 9 on firewire or the ATA card. DiskWarrior 3.0.3 reports that there is no blessed System Folder. Although DiskWarrior prompts to assign blessed folder, it does not solve the problem. However, when the disk is mounted in 9, the System Folder displays the icon indicating that it is blessed. There may be a problem with DiskWarrior here, also.
Note: When the backup copy is copied to another disk (120GB, not 250GB), the new copy behaves normally and boots in OS X or OS 9 with no problems. (The new copy was made after the backup copy was booted on firewire, however.)
These issues may still be somewhat hardware-specific due to using a large drive, but the OS X anomalies seem to indicate there are other problems that may still be SuperDuper-related, as far as having a good copy which is capable of booting up normally in OS X.
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