Link for hidden menu in 2011+ OEM HU:
In that thread you can find that it's possible to put the EQ in Through mode (which proven to be flat EQ).
If using the factory wires resulting in the system not at full potential then I think I'll just run quality speaker wires to the amp. The JBL MS-A1004 is built to accept both low and high level signals safely (or at least I hope a $500 class D amplifier should be safe) so I will be running the amp with high level inputs. The amp comes with adapters to turn the stock HU harnesses into RCA plugs. I will do a VERY detail video/picture installation of this once I have the car.
Now I need help finding a good place to mount this amp. It needs to be accessible so I can adjust the EQ settings. I'm thinking my truck space is the best but it would get in the way if I was to need the space to transport something big. Any other idea? I also thought about under the passenger seat but space it so I can access those buttons by pulling the passenger seat all the way back or something like that.
Ahhh the more I do research on this stuff the more anxious I'm getting with the wait of my car. The car won't be around until at least January 2013 T.T
Also I like to thanks all the helpful resources and supports of this forum. I went from a complete noob and scare of DYI car audio installation to confidence I can put all this together with ease. The only thing I would have tough time with is wires management, crossover location, and speaker spacers installation.