[robespierre]

The repeated Unit Not Ready messages are the result of the Indy resetting the SCSI bus and then trying to access the drive before it becomes ready (CD-ROM drives take a long time to become ready).
The real issue is the "Command 0x28 Unexpected info phase 49". Command 0x28 is READ (10). So during a READ command, a bus event (phase 49?) happened that was unexpected by the Indy.

Bus phases are a low-level detail of the SCSI protocol and this should not happen. Possible causes: interference by another device on the bus, or a difference in interpretation of which level of SCSI standard is to be used (asynchronous or synchronous, slow or fast, ....) between the Indy and the drive.

Termination or bus length may possibly be the issue. Do you have the Yamaha drive manual, and what does it say the "Termination" switch does? Does it activate an active termination feature of the drive? Is it in fact, wired to the drive at all?
Does the drive have passive termination (SIP resistor pack: attached image) or the sockets where it can be installed?
Is your external terminator a passive or active type?

On the Indy there is only one SCSI bus, used for both internal and external devices. But there are two SCSI ports, an internal port where a ribbon cable may be attached, and an external port. To make this work, the Indy's SCSI controller or "HBA" (host bus adapter) is connected in between the two ports. This is a special arrangement that means that both the last internal device (such as hard disk or Floptical) and the last external device (such as CDROM), and only these must have terminators or internal termination activated. The HBA itself does not provide any termination, as many other computers do.