The 'correct' way to do this (if I understand what you want to do) is to have a midi pedal switch that can change channels (e.g when pressed = Ch1, when not pressed = Ch2). Set the Midijay RECEIVE channels as follows. Right=Ch2. Left=Ch1.
This way, when you press the GUITAR pedal and play a chord on the Midi Guitar, it changes the Arrangement (equivalent to a keyboard player's left hand), when you don't press the pedal and play anything on the Guitar, you're simply playing notes.
The other way (better with the XD3) is to use the K8 Midipedal to trigger the major chords and use the volume tonality pedal to add the minors, dim, 7ths ... etc. This is the only TRUE way where you can play AND change chords together - a lot smoother than others ... it will just take some 'footwork' to do.