There is an alternate route to your goal than ctcs advice. That is, instead of setting each factor to thier own channel, set them all to listen to the same channel, sending out simple "program 1, program 2, program 3" messages, and tell each pedal how they should interpret those program change messages in the MIDI map. So "program change 1" will send the ModFactor to 6:1, while the same message on the same channel will send the TimeFactor to 4:2. I do it this way for two reasons. #1, the interface on my controller is more cumbersome and less intuitive than the MIDI map interface in the factor pedals, and #2, I notice an ever so slight latency, or delay, between the commands sent out by my foot controller, whereas when the factors listen for the same channel, the changes are completely in sync.
I don't know how the tuner works in the PF, so I cannot comment too much, but suppose I would do it in a similar way. Send out a CC message and tell each factor how to interpret that message. Then "CC 19" (or whatever you want to send out) can mean "Tuner" to the PF, while meaning "Bypass" to everything else.
