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Well, it's my understanding that if I program a patch (at least in my case) in PC mode with the FC-300, it should enable all the factors that are part of that patch by default.
Well, the FC-300 will send out one or more program change messages, and your Factor pedals will respond to that program change message by loading the preset its assigned to (if any) and if that preset was saved in active state it will be loaded as active and if it's saved as bypassed it will be loaded as bypassed. If your presets are being loaded as bypassed and you don't want them to be, you should activate them and resave them and see if that makes a difference when they receive the same program change message. Another possibility is that they may be receiving a MIDI CC or program change message that is bypassing them as they can be configured to respond to MIDI CCs or program change messages in this manner. If you hook your Factor pedals up to H9 Control, it will make it quick and easy to check these assignments.
If I were having problems getting my rig set-up with MIDI I'd probably use Midi Monitor on a Mac or Midi OX on Windows to look at what's coming out of my FC-300 to check that it's what I expected and go on down the chain to make sure each stompbox is sending and receiving what I expected. It might not be possible to fix the problem if you're not sure what each stompbox is actually receiving.
I would also like to know how I could go about using the built-in expression pedals to control some parameters on the factors via midi.
The expression pedals will send out MIDI CC. You'll want to figure out what MIDI CC they are sending out and assign that MIDI CC to control either the expression pedal patch or individual parameters on the stompbox, or you can use the learn function you mentioned earlier to have the stompbox listen for the incoming CC messages and use their CC channel. You can do this in your stompbox's system setting's screen under the RCV CTL menu. You can also set this up in H9 Control under Pedal / Midi Settings / Assign MIDI CC Messages to pedal functions.