Okay, well at the very least I'll likely remove the factory speaker wiring harnesses, since I won't need them, and having unused wiring harnesses there will just mess with my OCD! I'll run it by Don as well though, since I'm sure he has some first hand experience.
Sorry I could be more helpful on this as I can't remember the full harness, and if any other wires go through the harness, but I think you can cut and remove it, I just don't want to tell you to remove since I 100% cannot recall.