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I may be a little late here, but I'm curious as to what went wrong with the process. My first thought is that the the MIDI channels can be set independently for the footswitch CC values and each expression pedal in the FCB-1010 (as well as the Note value). From other posts, I see that your footswitch process was successful. That leads me to focusing on the expression pedal MIDI channel(s).
To review the FCB-1010 Global setup:
Press DOWN while powering up the FCB-1010.
Press UP to confirm the current Direct Select setting.
Press Switch 8 [Exp A] or Switch 9 [Exp B] until it flashes.
Press UP, and select the MIDI channel. Press DOWN 2.5 seconds to exit.
Now, of course, your RCV CH in the ModFactor should match the FCB-1010's switch CC and expression pedal(s) channel. I'll use MIDI Channel 1 and CC #7 for the expression pedal as examples. There's a way to "test" your FCB-1010 transmission within the ModFactor.
Switch CCs + exp. pedals on FCB-1010 + Modfactor receiving end = same MIDI channel.
Check that the ModFactor's MIDI -> OUTPUT = THRU.Show More...
Go to MIDI -> RCV CTL, and dial up the PDL entry.
Press the MF right footswitch twice, to the LEARN display.
Move your FCB-1010 expression pedal.
If the "connection" is made, the MF display will snap to CC7 (for example).
If everything is good to this point, move on to the ModFactor setup. Disclaimer: I use my FCB-1010 with a PitchFactor. But from the MF manual, it appears that you need to select the Q-Wah algorithm (or a preset with that), and turn the Shape knob to the pedal entry. Apparently, the usual pedal programming is done for you in this case.
I can see another potential way to control the wah over MIDI. The Xnob controls the base frequency of the wah effect. So, it looks like you could go to MIDI -> RCV CTL, select KB5, match that to your expression pedal CC number, and control the wah base frequency directly.