Yeah, i thought about it some more, that seperate fiber cable MAY be for if you install a phone, but don't have a fiber optics component in the trunk (Bose amp or teleaid).
Radio
Bose amp
Phone PSE
Teleaid
VRU
CD

The red vs clear lense is for id purposes only, the red lens ALWAY goes towards the chamfered side of the connector.
Occasionally the black plastic connector has to be seperated to allow proper configuration of the fiber optics line.
If you have the factory BOse, the amp in the rear should also be on the fiber optics loop at some point, as should the teleaid control unit.
If the single fiber optics line is connected to the PSE it's because YOU connected it, as the PSE is part of the phone install kit. I recommend disconnecting it at this point until you figure out the routing.
Where is the spare loop labelled SDS? In the rear? Is that laying across the trunk just ahead of the spare in that plastic tray?
It sounds like you are on the right track so far, in regards to testing the fiber optics with a flashlight and understanding that you have to maintain the loop (daisy chain) back to the radio.
I'm not familair with (or at least can't remember) what component SDS would be, I'm sure it's not a reference to star Diagnosis System. Maybe it means Sound System? This to me would refer to the Bose amp.
I could probably get you some better info later in the week, this is the best I can do on a Sunday afternoon.

Gilly