Considering the concept of foot diving through Factor stomps, it seems to me that one has to do a serious preset customising for live use, especially if more than one Factor is in chain. And if one does so, than it seems to me that it is much more comfortable to control Factors with MIDI foot device, and to patch them in efx loop section rather than before the preamp section. That would be my suggested answer to your dilemma. However, this is how I plan to organise my TF and MF in my live setup, and I have to do it in next few weeks, so I am interested in various approaches. If you have a better idea, I would appreciate to hear it.

All the best.