Not sure if this helps your issue but the 3 series/M3 guys including myself have to deal with creaks from the window/door seals. every time the car flexes you it would make a ton of creaking/popping noises and its all from the where the top of the doors meets the black shadow line trim when you close the door.
Adding a thin layer of this all around the area as well as the door seals (all around) eliminated all of the noises on my M3. even if it doesn't help this stuff is excellent at keeping all your seals lubed up and does not just wash off.
https://www.amazon.com/gp/product/B0...?ie=UTF8&psc=1