OK going to hit the high points quickly:
If you are referring to this drive:
https://hifiduino.files.wordpress.com/20...c_rev1.pdf
You will never be able to boot Irix media, nor read Irix-only application CDs. This drive does not have support 512 Byte block mode (no rear jumper for it). It will work with Audio CDs and normal ISO9660 stuff using normal 1024 byte block mode. But it will never install Irix using it nor read Irix-only media. It's not able to support reading CDs like a hard drive (common trick for SUN and SGI stations).
The separate black connector you mention is for automatically setting the CDROM SCSI ID... I detail that here:http://forums.irixnet.org/thread-1485.html
If you want to use it, you'll have to re-pin it (swap pins). However, since the Indigo2 only has one 5.25" drive bay...no one really uses it. Your CDROM drive should be set to SCSI ID 3 for convention, you should do that manually using jumpers on the drive. You may also need to set the jumpers to enable parity to be in full compliance (HDDs too) The front bays are SCSI ID 1,2,3 from lower right, moving up. Technically you can use ID 6 if you want (no harm). But must Irix instructions for typing in commands assume ID is 3 for Indigo2. Just saying.
No SGI supports taking Audio from a CDROM/DVDROM from the audio connector on the back of the drives. It's all digital, always. No on-drive audio decoding is used or supported. You need to run an app that supports digital audio playing (no CDROM-side decoding). I thought there were a few players in OSS.
The tray issue is purely a hardware issue with your drive. It might be a weak/loose belt in your drive system that has trouble lifting the tray up for ejection when in the vertical position, it also could be a drive that when you have media in the tray... it always fails to open when vertical and because the media gets jammed, saw this many moons ago). You'd have to re-oil with (plastic safe) oil/grease it and possibly change out the belt (not easy) to confirm this.
While I have a couple 5.25" Indigo2 trays with DVD drives. I use them so rarely that I'd always advise an external optical drive (like an old SUN drive works great) so you can share them among your SGI machines (should you get others).
DO NOT INSTALL A mechanical hard drive on the 5.25" sled, the manual says explicitly not to do that, drive will likely overheat and burn out. If you come across a flash disk that works, fine. Just don't use the 5.25" bay for mechanical drives, anything else is fine, like FLASH SCSI readers, etc...
Good luck.
NEED -> 