Sounds like you may have damaged the Head Units earth tracks....
Will assume you haven't located the source of your interference yet, so here's a post from a thread I did on another forum....
Background noise/Alternator whine....
To sort this you need to actually locate the source of the noise....
Is the noise only present with the engine running....
YES---Then its going to be a ground loop scenario, in 90% of cases its poor amplifier earthing that's the root cause....
Amplifiers should be earthed to the boot floor using good quality connectors, the earth site should be cleaned back to bare metal and once tightened treated against corrosion....
NO---Then chances are its down to a faulty item.....
With system switched OFF....
Remove the RCA leads from the affected amplifier....
Switch system on and play as normal....is the noise still present??
YES---Then its an amplifier or associated wiring fault, (Speaker cable pinched & shorting?? Speaker terminal shorting to a door panel?? etc etc)
NO---Then the fault is before the amplification stage, carry on...
With system switched OFF...
Refit the RCA leads into the amp, remove the head unit from the dash and remove the RCA leads from the back of it....
Switch system on and play as normal....is the noise still present??
YES---Then its a faulty RCA lead, simply replace the affected lead.....
NO---This would indicate you are using a PIONEER head unit which at some point has been connected up or disconnected incorrectly which has caused an earth track fault,(it can affect other brands, but the main culprit is PIONEER)...
To get round this fault,(it's not a repair, it's simply a quick fix), you should do the following;
Run a fused direct live,(20amp cable fused at 15amps), from the battery to the head unit,(essentially bypassing the audio looms constant live). you should leave in place the ign live so the unit operates as it should on the ign...
Run the head units earth,(again bypassing the stock audio loom), direct to the cars chassis,(use 20amp cable & ensure you select a good earth site and clean the area back to bare metal), the condition of this earth site will affect the success of this quick fix...
You will now need to earth the RCA plugs outer sleeves to the head units chassis,(i usually use the head units rear support screw location), this fix should solve most cases, but on occasion it can be necasary to also earth the head units mounting cage to the cars chassis....
