Thanks for your replies folks....
Thomas first:
Yes, I have tried using disk utility after starting from my normal drive, but am unable to verify or repair. Both buttons are dimmed. The dialogue actually says that you can't verify or repair the startup drive. I also see no option to "repair disk permissions" from there.
I don't know what it means to "delete Receipts", so I can't be sure about that.
Bruce:
I tried your suggestion and booted from the new Panther disk #1 and successfully repaired the volume (why wouldn't it work with the 10.1.4 CD???).
I then booted up from my normal drive (as recommended in the MacFixit article) and ran Disk Utility from there but still unable to do anything (and no sign of a "repair disk permissions" option).