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No, the green blank on the back of the MCS should pull out and then you can insert your black fiber optic connector.
There is no activation needed for the MCS. When you turn it on, it should light up at least one side. If its not sending the wakeup signal, it is probably a defective unit. The MCS will send a wakeup as soon as the power is turned on.
You only have to version code the radio to get rid of some fault codes concerning the actual and specified configuration of the D2B ring. I have replaced many of MCS units and they always worked when plugged in, I proceeded to version code them after it was working. Are you sure there is not another component taking down the D2B ring? If one component is malfunctioning, the whole entire system is down.
I usually have problems with the tele-aid module underneath the back of the passenger seat. I disconnect the fiber optic connector and install a looper/jump connector.
Did you buy the MCS used?
I agree with you that everything else should be fine since just the FM was out. That is a common problem with the MCS. I suggest you try exchanging the unit for another one.
cd player should eject even with no light signal. It's controlled directly by the eject button so that seems unusual. I think you have an intermittent problem. Does the eject button light illuminate on the cd player? It should if it has a good power and ground.