Your 3.9 Emergency Disk should enable your CD-ROM. Try booting from the Emergency Disk with your OS3.9 CD in the drive. Can you see your CD-ROM now?
Now use HDToolBox from the Emergency Disk to create your partitions, then run OS3.9 setup from the CD to install the OS to the hard disk.
Once the OS is installed it will copy the working CD-ROM drivers and mountlist to your hard disk. All you need to do is reboot and it will work. You shouldn't need to copy any drivers as long as the CD-ROM works from the Emergency Disk.
--
moto