>It seems like I did something that killed the second bus (ata bus 01).  
>I've switched devices and cables around enough now to know that the 
>only thing that seems not to work right is the bus itself.

A failed or bad installation of X can kill an EIDE bus, so it is possible 
to do just by software.

To try and get back the bus, power on the machine, doing the Cmd-Opt-P-R 
reset at least ten times (listen for ten chimes), then allow the machine 
to completely boot.

If the devices (more than just the EIDE buses can be affected) are not 
back, then the mobo may be toast.

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