Well boys and girls, the noise is finally gone. And while this fix is not up to my original standards, I am content and done with this project.
Here's the story:
I knew the AudioControl Matrix was intended to be placed as close as possible to the HU, but there simply is not enough room to put it in the passenger kick panel, and I didn't feel like mounting it under the seat. So for testing purposes, I just put it in the trunk with the amps. I tried it on every setting possible, and the noise was not reduced at all (if anything, it was increased on certain settings).
So out of desperation, I removed the Matrix, and just started trying random things. I plugged my iPhone into the RCAs at the passenger kick panel, but ALSO connected it to the car charger. Under these conditions, the noise WAS present with the alternative source (not nearly as bad, but present nonetheless).
This led me to believe that there was, in fact, a ground loop occurring somewhere further down the signal path. For whatever reason, I decided to plug in the PAC SNI-1 ground loop isolator at the passenger kick panel. I tried this $10 device months ago and saw no positive results. But miraculously, it worked this time. I isolated both front channels, and the noise was 95% gone (literally had to put my ear up to the tweeter to hear it). At this time, the gains on my amp were still set for my iPhone. I checked with a DMM, and the amp was putting out 15 volts, while my speakers can take 22.3v. I decided to keep the gains where they were, because I assume that increasing them would make the noise apparent again. Using Ohm's law, my speakers are rated to receive 22.3 volts at 4 ohms (125 watts). Since the amp is only putting out 15 volts at 4 ohms now, the speakers are getting 56 watts.
I'm not thrilled that my speakers are not reaching their full potential in terms of volume, but they still sound incredible, and get VERY loud. And who knows, maybe the GLI would still keep the noise down even at 22.3 volts. I might try that later.
I'll keep this thread updated with any future findings. Thanks for all the advice!