Basically it's only the icons which goes wrong when installing from OS < 3.5. You only need the new icon.library being active, then it will work. For example you could do the OS 3.5 "pre" installation and then install OS 3.9 full. Or as I said above, just install OS 3.9, reboot and install again.
The emergency disk will just save you a lot of disk changes and manual installation once you have it working. The emergency disk makes the OS 3.1 disks obsolete.
Bye,
Thomas