You cannot put a filter between the alternator and the battery - unless it had a 150A capacity. Your issue with whine is due to the interface design and grounding, not the stock electrical system.

I suspect the noise issue is due to the specific interface you have and how its chassis could be touching metal. You could start my making sure no metal on the interface is touching any metal in the car. A noise filter would be small (3A or so) and would go between the factory radio harness and the interface - meaning you would have to cut and intercept those wires (power and ground).

Big 3 grounding helps lower resistance but I doubt it would help your situation at all, and would just direct funds elsewhere. I would install a better quality interface before spending money on the Big 3.

 

Thanks for answering

I think you are right. I pulled the battery to chassis ground on the vehicle. I shined it up, made sure it was metal to metal and it did not change the problem at all.By this do you mean that I should pull the dasboard apart again, make sure the connectors of the MP3 kit are pushed all the way into the Aux input on the radio , and then make sure that the kit's cords are not next to a power cord or touching any metal. Also, the kit itself has several pins and plugs into the radio, but I should make sure the kit itself (the plastic connector) is not resting against any metal.

If I do that and the whine is still there, then I would put a noise filter between the where my MP3 kit attaches to the radio and my MP3 device.

So:
Radio > Aux Kit > Wire > Filter > more Wire> MP3 device

All of this because I am layed off and want/need to do it the cheap way. Thanks for hanging in there with me friend, its been a long road

 

Your methods are sound. Those are the steps I would take. With a noise filter you should be able to get an install that works as you intend. Pay careful attention to how wires are routed, and how metal surfaces are isolated.