I just felt it would be good to share this as I searched quite a bit and only found small amounts of info. I have a 97 A4 1.8T Quattro and it has the Bose amp in the trunk and I really wanted an updated stereo. I went out and got one and after pulling everything apart realized it had the stock amp that would pose an issue. I have dealt with Bose amps and the Capacitor arrays in the past by taking them out of the loop completely but this time I was not able to easily take that approach as I would lose use of the two back door speakers which I preferred all to be working.
I messed with the wiring but never could get past the pop when turning down the volume to 0 or taking the key out of the ignition, so I ended up giving up and running all new wires to 4 of the speakers and called it a day. Over time this became an issue as the sound quality sucked with the custom Bose impedance’s. After about a year I sought out a harness that had the RCA cables converted instead of my hacked cable job, I found one on eBay and was ordered it up from a company called DNF (HEADUNIT ADAPTER 1005). I got my harness and happily reconnected all the stock connections and fired up the stereo and painful to my ears I hear a nice loud POP, after a lot of choice words I realized my issue was not the hacked harness but the fact that most aftermarket head units ground the RCA jacks to the ground wire of the unit creating a common ground instead of a floating ground.
So this is where I started my research and found the issue is because the capacitor array that cleans up the unwanted sounds gets grounded out causing them to release energy quickly. I then started looking into options to create a floating ground from the RCA’s to the Bose amp. After a while I found something called a “Ground Loop Isolator” great device I must add. I found they sell these at best buy for $14.99 and many other places, so I went and picked two up and tested them out. After adding them I no longer have any issues with pops and the unit is passing crystal clear audio through the stock setup.
I hope this long winded story may help any one finding them self in a similar pickle, Thanks.