Is there a straightforward way to use one controller device to activate both pitchbending on the Pitchfactor and modulation on the Modfactor separately via message filtering?
It depends what do you want to do because PitchFactor doesn't have a parameter called pitchbending and ModFactor has so many modulation parameters. But generally speaking, yes, you can.
I would suggest you connect your PitchFactor or ModFactor to your computer through a USB cable and use H9 Control to edit the parameter and MIDI mappings.
1. You need to figure out what MIDI messages your Yamaha MCS2 is sending when you control the PITCH BEND, MODULATION, or other controls on MCS2.
2. Edit the MIDI mappings:
If you operate on the unit, you can edit MIDI settings by preset and hold the encoder and right footswitch to go into settings, turn and press encoder to go into sub menus: Settings->MIDI->RCV CTL. Then you can map the functions with Pitchbend or according MIDI CC messages from MCS2.Show More...
If you use H9 Control, after successfully connecting the unit to H9 Control, you can go to Pedal Settings->MIDI Settings->Assign MIDI CC messages to pedal functions->some function. Here the function you want to assign should be expression pedal value or a parameter's value. It depends on what algorithm are you using and what kind of sound do you want. You can edit the expression pedal mappings easily in the Presets screen in H9 Control. Please see attachments for more detail.
You don't have to use MIDI message filtering. You can just connect your MCS2 to PitchFactor, and your PitchFactor's MIDI out to ModFactor's MIDI in. And assign PITCH BEND (or any other controls' MIDI CC messages) to PitchFatcor and MODULATION's CC message to ModFactor.