audio interference

[Modo Innovations]

Most of the time your issue is caused by a poor ground. You stated that your head unit uses the factory harness, I would ground it to bare metal close to the unit instead of using the factory harness ground. Also look at your RCA cables, are they routed close to any power wires for your ignition control box? This can cause interference issues as well. I hope this helps. There is nothing worse than having noise in a nice stereo system, it's such a bummer.