I now believe that what you have been dealing with is a electro magnetic feed back waves.

The ECM it self emits those waves but since the RCA cables are quite close & carries the signal processed by the head unit they might have being "receiving" those waves from the ECM.

Try to place those RCA cables on the opposite side,if you have the means $$$$$$ have those cables upgraded,the twisted or braided RCA cables works better for this kind of situations.

Hope this one works for you buddy