I forgot that the Mac itself shows up at ID 7 - so you should have 3 IDs showing.
OK. Here's my theory.
The SCSI cable on these cases (IIvx, Quadra 650 etc) is VERY short.
When you disassemble the machine, and lift the large metal drive cradle, the SCSI cable can become unplugged. Sometimes only one side is lifted, and it generally looks fine when it does.
The cradle only needs to be lifted about an inch for the cable to be pulled out. Not only that but putting the cable back into the motherboard socket is a REAL PAIN IN THE A$#. IIRC, it has a stupid miss-alignment with the CDROM socket so the cable is strained to one side. The floppy cable also creates great interference with the SCSI cable. It's a really bad design.
Be very careful of this chassis - it can slice your hands quite easily. Rumor has it that it was so bad that it resulted in the 7200/7500 style case that was more technician friendly.
The most likely problem is the connector on the back of the CDROM drive. You'll see that it's a strain from the SCSI drive to the CDROM drive. The floppy cable has to pass in front of the SCSI cable to reach the motherboard connector too.
EDIT: This may help in disassembly: Note that the power supply MUST be removed to lift the drive cradle.
http://www.micromac.com/instructions/P600_2_Q650/index.html