I figured out how to load a song when mounting/dismounting a chocobo, but in the meantime it'll be the battle fanfare.
I've noticed the music engine patch messes up the music and sound effects. I understand that you changed the entire scale, but among other things it sounds weird when lightning attacks now sound like birds chirping (Chidori™ (千鳥)???)
When I open a MIDI I pick the best Melody channel as Sq1, Harmony/Accompaniment as Sq2, Bass/"Atmospheric" as Tri, and Percussion as Noise, remove the other channels or move certain notes to the main channels. Each channel will only hold one note at a time, but MIDI can hold more, so you have to remove all overlaps.