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Besides MIDI Transimit, there is another setting called PGM.XMT or something similar, you would need to turn that on as well.
You can set the aux switch midi mapping by going to the Setting Menu by pressing the encoder and the right footswitch, then go to MIDI -> XMT CC -> TIP or RNG or T+R, then set the mappings there (like C100, C101, C102). Then you would need to go the the MIDI setting on your ModFactor, and in [RCV CTL] – Receive Continuous Control Message, assign those MIDI messages to the functions you'd like to use.
Page 51 has some useful info for you: https://s3.amazonaws.com/com.eventide.downloads/Product+Manuals/TimeFactorManual.pdf