Aod,
Lets start withe the alternator whine. What you need is a 3300 microfaraday axial capacitor.
http://www.radioshack.com/product/index.jsp?productId=12424820
This capacitor is wired on the output of the alternator and grounded on to the side of the alternator (one of the alt. housing bolt). Make sure arrow on the side of the capacitor is from the pos. to ground (current flow). 90% sure this will take out the whine.
As for the popping when the head unit is turned on or off, you need ground loop isolators.
http://www.ebay.com/itm/3-5MM-GROUND...item27c52360c8
To use this you will have to use Metra harness since you need RCA connection to splice this in. Also, you will need two ground loop isolators since your head unit has right/left for front and right/left channels for rear speakers. You do not need to ground out (two brown wires) isolators. Ground loop isolators are sort of miniture transformers and will allow low level audio signal from the head unit to your amps and yet not allow electronic noise generated between various ground points on your chasis and mistaking temporay voltage difference when the car is turned on or off as an audio signal.
I recently installed a Pioneer AVIC Z140BH and spliced into OEM Bose amp/speakers and experienced on/off pop. Ground loop isolators took care of this annoying noise.
Try these two remedies and post the result. If any other noise remains we can address it.
Good luck!