Big update. I fixed it. I had it wired 100% correct, but the fact that the amplifier is CANBUS controlled meant that I couldn't control it with any amount of relays or timer circuits. I read about a similar case where a gentleman with a Lexus IS350 had the exact same problem, I used his solution to fix it.
I used a Cache Audio COE8EQ as a line output converter to send low level signal to the MS8 instead of using the high level inputs. The conversion from high level inputs to low level keeps any power on/off pops from the Sony amp from being passed through to the MS8. So it works perfect now, sounds great too.
I just need to build a better mounting bracket for my gear. The good news is that I am free to upgrade the rest of the system whenever I get the time and motivation.
So the system is set up like this, Nav Headunit --->Sony AMP ---> COE8EQ ---> MS8 ---> Speakers
Its possible that there was a simpler way to do this, but this is the solution that I got to work.