Those extra MIDI CC messages are not originating with KymaConnect. The CC118, and other CC messages on channels 15 and 16 are from the Continuum's protocol. If you power off the Continuum those messages should cease.
The Continuum's "native Kyma" protocol uses CC11 for the Z-axis information. The Continuum can handle up to 16 simultaneous touches so it is possible for CC11 to originate on any channel. I believe that the Pacarana consumes all of the CC11 messages while in "Continuum mode" and they never reach the VCS. This also applies to CC74, which is used by the Continuum in native Kyma mode for the Y-axis (MPE uses this as well). Those CCs are just not available for VCS or other duties when Kyma is controlled by the Continuum using the native Kyma protocol.
This is not part of your problem, but for the sake of completeness, the Pacarana will also consume all channel 1 CCs when Kyma's VCS is set up in MotorMix mode.
MPE does not use CC11 (it uses channel Aftertouch for Z-access), but as I mentioned it does use CC74. You could gain use of the CC11 for your fader if you could coax Kyma and the Continuum both into MPE mode. I have done this through trial and error but it is not an easy, repeatable process. This is not the fault of Kyma or the Continuum but a reflection of the fact that MPE just became an official standard recently and there devices with different interpretations, of different versions of the MPE spec, out in the wild. So while it is possible to use the Continuum as a MPE controller for Kyma I can't really recommend it now as a work around for your fader issue. Besides, the Continuum and Kyma work so well together when using the native Kyma mode it would be hard to give that up.