"I take this to mean it is not a hardware issue."
How can you be so sure? We use a dead Zip Drive as a cable adapter. The read head is dead but the signal passes through. Even when SCSI Probe sees the device, it does not mean that the device is still OK.
If you can find an external SCSI enclosure, you can test it on the external chain. The fact that the Zip drive still works should indicate that the chain is OK but ruling out all possibilities is helpful.
If you try and boot from an install CD, will the drive be recognized? Try that next. That should help isolate software issues.
In the 9600, the internal SCSI hard drive, CD-ROM drive, and Zip drive occupied the same "Bus 0" and ribbon cable. Traditionally, the hard drive was the last device connected to the ribbon cable and had its "Termination Enabled" (TE) jumper installed. When you opted for the ATA controller card/IDE hard drive(s), did you disconnect the original hard drive? If so, did you install a termination jumper on the Zip drive? The OEM Matshita CD-ROM drive has a "TERM PWR" jumper installed by default, but this isn't the same thing as a "TE" jumper. If you haven't done so, you need to terminate the SCSI bus via the Zip drive or install a terminator in the next available ribbon cable connector after the Zip drive.
Jeff got me thinking about the internal ribbon. This website at MacGurus offers motherboard layouts. Were there two internal SCSI ribbons, Zip and CD on one chain? The diagram does not label both. The G3 had one SCSI and one IDE ribbon connector and they are different sizes and are labeled. The diagram for the 9600 shows two equal ribbon connectors. Be sure and verify that each SCSI chain is terminated.
The Power Mac 9600s did have two SCSI buses: Bus 0 and Bus 1. Because SCSI Bus 1 was slower (SCSI-I speed - max. 5 MB/sec) and shared the external DB-25 port on the back of the computer, none of the internal drives were factory-connected to it. As a result, the internal hard, optical, and Zip drives were connected to a single ribbon cable on SCSI Bus 0 (SCSI-II speed - max. 10 MB/sec). The typical ribbon cable routing went from the motherboard to the optical drive, then to the Zip drive or second hard drive (if any), and ended at the main hard drive (SCSI address 0), with termination applied there. This was how all of the Power Macs with dual SCSI buses (7300, 7500, 7600, 8500, 8600, 9500, & 9600 models) were configured. A Build-to-Order configuration may have modified this scheme, but otherwise, it was standard. As shipped from the factory, if nothing is connected to the motherboard's SCSI Bus 1 connection, no terminator is needed.
There is JOY. By terminating the exterior bus I at least got the computer to recognize the optical drive, but...
After all these years with old Macs I still don't know what is important about SCSI termination - being physically located last along the cable, having the highest SCSI ID number, or both, or neither?
Thank you Jeff and Apaloosa mac man for your help.
The SCSI chain was a lot of power provided to a home computer. It contributed to the higher cost of the computer. It also added to the longevity of the hardware usefulness and ease of use. It was decades before a PC could boot from an external device the way a Mac could in the '80s.
Here is what matters in SCSI.
1. It is not plug and play until configured. Each device has to be configured to a specific address. The benefit is the ability to have seven devices recognized at startup.
2. Termination. The signal needs to know when to stop searching. At startup, the host or computer will 'poll' the devices. The first device that it sees with a system folder will allow the computer to boot up. With 'Startup Disk' you can reassign that task to another system folder on another device. The benefit? You can easily repair one hard drive by booting from another drive. Termination tells the host that all devices have been accounted for and it can now move on to the task of reading a drive. Zapping the PRAM tells the host to start fresh and poll all devices. It takes longer to startup but it creates new directories, or table of contents, so to speak. Otherwise the computer may lose track of where to find a file.
3. The highest ID number just sets the priority or que during the device access. The higher the ID #, the sooner it comes in the polling process.
If you want to optimize your SCSI devices, study the rules programmed into the protocol, otherwise, just enjoy the fact that a Mac will let you swap out drives and reconfigure without a lot of trouble. A 'D' drive in a PC will not boot the computer, even if it is a carbon copy of the 'C' drive. In fact, change the C drive to the D drive location in an older PC and the PC will not start.
The external SCSI port was the greatest hardware tool Apple ever offered to the government surplus shopper. We would buy Macs at government auctions and test them within minutes with an external zip drive or hard drive. The PC guys would spend a day on each used PC because they had to find drivers for the video card, the network card, the hard drives, etc.. The SCSI chain was plug and play if we had our external drive set at ID 1 or our zip drive set at 5 because the internal drives were almost always still at the factory setting of 0.
Enjoy your mac and good luck with your optical drive.