I'm using 3.9, which I believe does not require IDEfix? So do I just change my CD0 mountlist to use atapi.device instead of scsi.device?
There is no atapi.device unless you install IDEfix. You need IDEfix to use more than two devices.
However, you don't need the IDEfix program. Atapi.device is part of the IDEfix package, as is the IDEfix program. To drive CD-ROMs, you only need atapi.device.
2. Will my existing Emergency disk still work if I make the same modification to the CD0 mountlist?
No, you have to make the same changes to the mountlist on the disk. And you have to copy atapi.device to the disk if you use it.
3. For fresh 3.9 installs, do I have to install 3.1 first, then IDEfix, then upgrade to 3.9?
If your emergency disk works, you don't need 3.1. So make sure it works and you are fine.
Bye,
Thomas