I'd really just used Soundbox at first because I'd seen mention of its use on the boards here. It seemed like the MIDI files could be imported directly without issue, so I wasn't sure if Soundbox was advised for any specific reason. When I decided to add loop points to them, though, it looked like Soundbox was again necessary, since I think the Companion editor only allows enabling and disabling of existing loop points?
It's also all brand new. I've started working on the MIDIs themselves a couple of weeks ago, but just started monkeying with them and the game last week. That and my status as not-really-any-kind-of-programmer makes it all a real learning experience. I am positive that I'm doing most things pretty ugly while learning the ropes.

The driver theory sounds pretty reasonable, if also like something that'll guarantee the need to rethink the attack.