I actually had a similar problem recently. I have an A4000D and I am using a Dataflyer 500/2000 card from my old A500 as a SCSI interface. My SCSI CD-ROM drive never showed up in HDToolBox. What you need to do, if you have a PC available, is insert the 3.9 CD and go to the "Install 3.9" directory. Inside there will be a CDFS something directory.
I recommend making an LHA archive of those files on the PC. If you cannot, go ahead and copy the files over to a floppy but be warned unless you have the retail version of CrossDOS you will not be able to see Windows long filenames which would make your files 7 characters long with a ~ plus a . plus the file extension. Its a nightmare. If you cant find LHA for the PC try using UAE.
This sounds like a pain in the ass but in the long run you need the files in that directory because they contain the installer for the CD-ROM driver. Now during the install of the CD-ROM driver software it has a detection software that shows you the #?.device drivers from your DEVS: directory. Click on the one from the GVP device you are using and it will show you all SCSI devices including your CD-ROM drive. Click on the CD-ROM drive and it will create a mountlist entry for you that appears on boot.
The next time you boot your machine you will see the OS3.9 CD in all it's uncolored unsupported glowicons glory. From this point it is easy to create the boot disk necessary or do an install.
Good luck
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