Happy to hear that you've solved it, but I still feel like I'm missing something here.
MIDI clock is (MIDI-) Channel independent. One clock controls over any/all MIDI Channels. Program Changes are per-MIDI Channel. To an outside observer, it seems like you could have your MIDI controller send (and the Timeline receive) on one specific MIDI channel. Then have the PitchFactor receive (nothing, really) on another MIDI Channel.
As I said, I may very well be missing something here.