These SLK's are really complex on the fiber optics. There are 2 sets of fiber optics, plus another jumper fiber optics from side to side in the trunk. The original configuration is basically a non-useable configuration. You need to reconfigure not only the 2 that you need to use in the trunk, but also there are extras behind the radio that have to be reconfigured. The reason for all this is that the fiber optics have to be able to be set up for either the CD changer only, the phone only, or both the CD and phone.
The phone components would mount in the left side of the trunk if you had it, so things get a little confusing.
If you had just the phone, you'd need the pair going from the radio to the left side of the trunk. To have just the CD like you want, you need a pair from the radio to the right side of the trunk. To have both, one fiber optics line goes to the right side, then uses this "jumper" line to go from the right side of the trun to the left side, then one from the left side back to the radio. Easy, huh?
In addition to that, yes there is a programming change required so that the radio will "know" that there is a cd changer present.
If you can get the radio removed (required a cheap pair of special tool "keys" to remove the radio) then maybe I can help you get the fiber optics straightened out, but you should get this programming changed in the radio too. Without it, it may work OK for awhile, but ultimately it's going to need it changed or the whole thing can quit on you (the sound system anyways)