The Musicomlab EFX switcher has Midi functionality so you could use the loops on that that for your mono pedals, and switch the 'Factors with Midi, and then you don't need to put them in the loops at all. Admitidly I haven't thought through how you would wire it all but definately worth thinking about. Midi makes the factor pedals so much nicer to use. The Musicomlab can also switch your amps channels as well, so you can send progam changes to the factors, switch pedals in/out and change the amps channel all with one press of a footswitch.
The Musicomlab is a very nice unit, very compact and the Midi is really easy to use.