Since I had no idea what the Acoustic FeedBack System is I just did a little search on google. I am still not too familiar, but found this interesting read. You are probably more knowledgeable and might find something in here...
http://personal.bellsouth.net/v/i/vi...ludeaudio.html
Since you say that the humming stops when you open the trunk lid, something with the placement of the hardware popped into my head. Do you have a wire pinched? Is your ground for the amp very soild?
If that doesnt solve anything, maybe you can see if you can bypass that AFBS and the amp for the rear speakers. I would just do a whole bunch of trial and error stuff. Keep us updated.