Let me cover how it is supposed to be wired, and you can compare your setup.
In general, the MS8 is the hub for EVERYTHING. All inputs must go to it, and all outputs must come from it. You need a remote turn on trigger (like the stock Sony subwoofer amp's turn on wire), but it doesn't need a full 12v if I remember what the manual said. That needs to go to the Remote IN portion of the MS8. All speaker wire inputs go to the MS8, and I chose all the channels and let the MS8 flatten and perfect the signal, which worked in my case. Side note, the head unit should be switched out of surround mode if it has the option. OK, so all inputs go to the MS8, and the outputs get redistributed back out to the proper speakers directly OR through amp(s). You can NOT run the same channel (let's say channel 1) on both the built-in power AND an amp with an RCA at the same time. You can also NOT do this with the inputs. Each channel needs to be either on its own power (20W @ 4 ohm, 30W @ 2 ohm), or with an RCA cable to an amp.
My concern is that you are powering the stock sub amp somehow. That's a total no-go, because the MS8 can't properly feed a signal to the stock equipment for playback.
If you don't have any amps right now, just use the stock MS8 power for everything, channel by channel. It isn't a ton of power but it is enough to at least get you good sound, and you can make sure all is well with the system before adding complications.
edit: I got a chance to read your report on this, and it sounds right. But apparently, that turn-on is wrong I think. I'm digging through the OEM manual now for a 2011 w/ sony.
While looking, be advised there is a rear parcel shelf speaker that is a CENTER channel for the rear, like a 6.1 DTS surround system could have. My 2010 Sony-equipped Flex had similar, it actually used two 3.5" speakers in the back pillars, but they were wired mono parallel. So it is similar. That speaker is green/brown + and violet/brown -
So the pin you should be connected to I think is pin 1, a violet/red wire.
Pin 3 is a SUBWOOFER wire! Its the Right Rear (think, single sub but dual voice coil) + output. THAT's IT!!!