To answer my own question.
I ended up cutting the wires about an inch down and stripped a few inches of insulation off to get the wires uniform, which actually cleared things up quite a bit. There is another set of wires insulated within the cord. That set was wrapped in insulation, paper, and stranded wire, which turns out to be the thicker black wire (they just cut part of it and wrapped a bit of it in insulation) and fits nicely in the only large hole for the PCB. I'm guessing that was probably the ground for the signal wires, which was what was inside. I already forgot the colors exactly, but there was definitely a red wire in that cluster. This inner set allowed differentiation between the black wires, and the red wires. One red wire was signal, and would then be routed to the headphone jack to power that even if the speakers are turned off. The other red(black stripe I believe) wire would then be the main power source, and it makes sense for that to go to the variable resistor (main sound control dial), so then it would provide power and a maximum voltage/signal value for the speakers, so just follow the PCB wiring to differentiate between power and signal red wires.
So going Left to right as viewed from the image.
blue, yellow/tan, black (or the wire sheathing around the signal wires - I used the insulation I cut off the cord for make-shift wire insulation), green, grey, brown, skip hole, white, red, black, red, purple.
Also, ironically, my speaker system used to occasionally pulse in volume/intensity every once in awhile. That doesn't seem to happen anymore.
Finally, some connections seem absolutely useless. They go to resistors that don't exist on the controller. My best guess is they used the same controller for a 7.1 system, but simply removed the two resistors to restrict the signal to only 5.1. It'd be interesting to take the sub apart and see if it can be semi-easily "upgraded" in a rather ad-hoc way.