I don't think the Emergency Disk will work even if you change the EMERGENCY_CD mountlist on it to the correct device/unit. This is because the floppy contains a copy of the AmigaOS ROM Update. Surely this is specific to the model of machine? So if you make the disk on an A4000, it will have the A4000's ROM Update, which probably wouldn't work too well on an A3000. A much better way of doing this is the following:
1. Install 3.1 to HDD from your Workbench floppies (or from UAE as suggested)
2. Configure the CD0 mountlist in 3.1 to correctly mount your CD drive
3. Insert the OS3.9 CD
4. Run the installer and choose the option to create an Emergency Disk
5. Boot from the Emergency Disk with the CD still in the drive
Simple :-)
--
moto
