Ok, hopefully I can describe this detailed enough.
I have a 09 electra glide standard. I added a kenwood head unit, mb quart 2 channel amp and 2 6.5 kicker speakers in the fairing. No issues.
Then i added lower fairings with 6.5 polk speakers and replaced the 2 channel amp with a 4 channel, soundstream stealth amp about a year later.
Sound was much better and louder with new amp.
Then i began to notice noise from the left fairing speaker. Thought it might be blown, but realized the noise wasn't in beat with the music. Ran the stereo with the engine off, no noise. Then noticed that it was engine noise. Some poppimg and low rumbling. Figured it wasn't the power wire to the amp, because all of the speakers would make the noise. I rerouted the speaker wire thinking maybe a wire in the fairing was interfering. I tested and all seemed fine until the next long ride. Thats when i realized it doesn't start right away, but sometimes after riding for a while. Seemed to notice noise increasing when i turned the handlebars with the motor running. Also thought i could hear some popping when the bike was on (not running) and i applied the front brake.
My ground is connected to a spot on the tree where to other wires are mounted. I think one may be for the lights?!
Is it the ground? Have read posts where guys say to run the ground to the battery. Have had people tell me not to run a ground right to the battery. Any ideas?

 

It never hurts to clean the ground contacts, especially if they are of any suspect...

And yet, my first guess would be 'white noise' caused by the ignition electronics. I'm no expert by any means, yet I would suggest a noise filter of some type. We used to install resistors on the coils of car engines to reduce the 'white noise' feeding back through the sound system. On computers, and other electronics, they sometimes use a carbon (?) ring that the power supply wires run through to reduce noise bleed over.