[jpstewart]

I attempt to install the CDROM drive through Indy's internal 50pin flat connector.
It detects as multiple CDROM Drives, it seems that is caused by no ID assignment for the drive.
If this is correct, is there any solution in order to use the drive?

Assign the CDROM an unused SCSI ID.  The controller in an SGI is always ID 0 (which is what your CDROM will be with no jumpers set).  Your SCSI2SD appears to be ID 1.  So jumper your CDROM drive to anything else.  You're using dksc(0,4,7) in your sample command, so I'd suggest jumpering the CDROM to ID 4.  Most SCSI drives have a label near the connector describing the jumpers.  If yours doesn't, you'll have to do a Google search for the manual for you specific model to figure out which pins to jumper to set the ID.  (They're usually between the SCSI and power connectors along with pins for other settings.)

It might also be possible to configure your SCSI2SD to emulate both a hard drive and a CDROM.  Check the SCSI2SD documentation for how to do that if your real CDROM doesn't work out.