Why would you delete all things in Devs:DOSDrivers, and CacheCDFS in L:?
In Devs:DOSDrivers are all the device drivers for Amiga, so you should only delete those which point at your CD drive, and in this case it would be those pointing at scsi.device unit 1.
CacheCDFS is the filesystem for CD drives, and without this your CD drive will not work.
To install OS3.9, make a working environment with CD support, insert the OS3.9 CD, create an emergency CD from the install script on the OS3.9 CD, reboot the computer and load OS3.9 of the nemly created disk, format the boot partition of the hdd and install OS3.9 on this.
-EDIT-
Choose NOT to install the device drivers, etc, from the Emergency disk. Instead, after the installationprocedure has finishing, boot from the Emergency disk again, and choose to install CDROM Support.