I have TH3, but a quick look at the THU manual indicates no changes in MIDI.
I also have the UNO chip, so what I tell you about the stock chip is 10 year old memories. If I send you an example sysex I'll be creating it manually with one of the editors that are compatible with the stock chip. BTW - what editor are you using?
The manual is pretty clear on establishing the connections to your Audio Interface and MIDI controller.
Your main consideration is logistical, as the THU MIDI implementation is just OK.
THU has LOTS of presets located in LOTS of BANKS.
Unfortunately, it doesn't allow for changing banks via MIDI. This means that the MIDI Option "Program Changes recall presets in the current Bank" means exactly that.
If you want to use a preset in a different bank, you'll need to change banks manually. The BANK switches on the FCB DO NOT transmit MIDI, and can't be used to switch THU Banks.
The best way to deal with this is to save all the presets you use regularly into a custom user bank. You can name it "My Presets" or some such.
The FCB allows access to 100 presets of the 128 allowed by the MIDI Spec. IIRC, a factory reset numbers the presets/pedals 1-100.
PC#s change presets. CC#s toggle effects. A given pedal can send a PC# and 2 CC#s (and other stuff not relevant to using THU) on load. Those 2 CCs can be set to toggle on successive presses of the pedal. You can use different CCs in different presets. You can also configure a pedal to sen ONLY the CCs without sending a PC.
THU allows you to toggle effects in CATEGORIES, not by specific effect. If you create a preset with two Overdrives, they'll both be toggled using the SAME CC#.
You can assign CC#s GLOBALLY or per preset. A globally assigned CC is overridden by a preset assigned CC.
So here's what you need to think about. Using the Stock Chip, in order to be able to toggle effects from each FCB bank, you need to decide how many effects vs how many presets you want to access from each bank. For instance, 5 toggles means 5 presets. In 10 banks, that limits you to accessing 50 presets.
You could also set up one bank for toggling 10 effects, and the other banks for presets, increasing the number of accessible presets to 90.
But then you'd have to return to that bank after selecting a preset in a different bank, which could require multiple presses.
Obviously, any combination is possible, but keep in mind that remembering a bunch of differently configured banks could be messy.
If you're interested in the UNO Chip, it allows you to to have 5 effects toggling pedals (the same CC#s) in each of 19 banks, each of which also allows access to 5 presets for a total of 95 presets.
I need to go out now, but think about it and get back to me when you have a plan.