I know this is an old thread but I think I can share some helpful info - I had this same problem with a similar setup (2011 328i / e90 + technic harness + JL XD600/6) and after banging my head on the wall for weeks here's what fixed it for me -
I took out my head unit (lots of videos on youtube) and wiggled the two big cables that plug into the back right of it. I assume one is antenna and the other is power or ground. With my wiggling I could hear the noise come and go, so I wrapped them in some electrical tape and put the head unit back with the cables in a position/tightness that did not cause noise. So far so good!
It's important to note that you should first diagnose if your problem is coming from before or after the RCA<->AMP connection by unplugging the RCAs and listening, and also plugging in a different source and listening. Hope this helps!
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