I would like to correct that problem, but have no idea why it would not find the CDROM.
At first you should connect your old HDD back to the Amiga and boot from it. Then put the OS 3.9 CD into the CD drive. Open a shell window and enter INFO. Check what the drive is called the CD is in (usually CD0: ). Now look into Devs: DosDrivers if there is a file of that name. Load it into a text editor and paste its contents into this thread.
Now insert the emergency disk, open Devs/DosDrivers on the disk and load the file EMERGENCY_CD into a text editor. Paste the contents here, too.
Basically we need to check if Device= and Unit= have the correct values for your hardware configuration and that the files named in Device= and FileSystem= exist on the emergency disk.