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How is your new headunit sending out its signal? Speaker level or rca line level? I presume the D2 bose is fully amped, so how are you sending a signal to the bose amp? The original headunit was probably sending a tiny pre amp signal to the bose amp to be amplified out to the speakers, now you may be sending an already amped signal out to be amplified by the bose amp again resulting in noise.

Again im not sure of the D2 setup but on other models like A4 A6 half amplified systems the front speakers were powered directly from the headunit and the rear speakers and sub were powered by an amp. You had to send a pre amp rca signal from the new headunit to the stock amp to cut out the buzzing and popping from the rear. The fronts were fine as they were already powered by speaker level output from the symphony or concert headunit.

Hope this makes sense. I've never tinkered with a bose system just the half amplified non bose versions and the fix for buzzing and popping noise on that was to cut an rca cable, connect the positives and grounds together, plug it into the pre amp rca port on the back of the new headunit and send it to the amp.

Edit just seen your pic and it looks like your cable is taking its signal at pre amp rca level. So ignore my babbling above. All i can say is make sure everything is tight and well connected, maybe ground the case of the pioneer to a good solid ground.