MF-103 | What is the difference between the Main audio output and the Aux audio output on the MF-103 Phaser?

The main output carries the original signal PLUS the phased signal. The Aux output carries the original signal MINUS the phased signal. Generally speaking, the Main output will have more high and low frequency response, while the Aux output will have more midrange. If both outputs are connected to a stereo sound system, you can hear a stereo effect where parts of the frequency spectrum move between the right and left channels.