To adz:
The Boot hard drive on a Commodore A2091 SCSI Controller card should always be set to device # 0. Also, what revision is the Western Digital controller chip, 03, 04, or 08? I think that a 40X CD-ROM drive may be too modern for the classic A2091 card. Try a slower drive, like a 4X to 16X. Make sure to check for terminator resister packs plugged into or soldered onto the drives logic board. Some CD-ROM drives have a jumper for disabling the termination. Also, are the resister packs still soldered on the A2091 board, near the 50-pin SCSI connecter? You have to remove them to get the rear port to work properly. :-P