You main problem is that you didn't access the OS 3.9 CD with Amiga CD-ROM drivers during installation, but added it as a harddrive directory. Because of this CD drivers have not been installed or installed incorrectly, some files have not been copied and most of the other files are marked write protected now.
In order to install OS 3.9 correctly, you should first create an emergency disk, then unprotect all files on the emergency disk and adjust the CD drivers to point to the correct CD drive. Then remove the CD drive from the list of harddrives, boot from the emergency disk and access the CD only through the drivers on the emergency disk.
Then you can install OS 3.9 without any problems. And with working CD drivers and sound.
Bye,
Thomas