Not quite sure what you mean by "bypass the Modfactor."
If you mean that you want the MIDI stuff to go into the MF input and come out of its output (i.e. pass through unchanged), you must set MIDI OUTPUT to THRU (see User Manual).
This does mean that the MF will not generate any MIDI – if you want it to do this you will need to connect a MIDI Merge box on its output, rather than the THRU.
