Ok
So its engine whine but whats causing this problem and lets see how I can fix it.
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Shielded RCA's
A good pair of shielded RCA's may be the easiest way to avoid engine noise. Don't use patch cables or other el-cheap-o RCA's that are unshielded. I'm not saying you need to invest a small fortune in RCA cables, just make sure they are shielded."
Im using Krystal KnuKonceptz RCA's, properly shielded...
"Proper head unit ground
This is perhaps the most common source of engine noise. Many times factory head unit grounds are poor. Relocating the ground wire or adding to the existing one will help reduce or eliminate ground loops."
I am using the factory head unit grounds but Ive never had an issue with it before with the sub woofers.
Proper amplifier ground
If none of the above have worked, check the ground for the amplifier. Make sure it is grounded to the frame, battery, or other substantial metal surface. Make sure the metal is good 'ol fashioned detroit iron. Many cars use metallic alloys or composites that aren't very conductive. Avoid those at all costs.
Amplifier ground works fine and is fine.
Wire routing
Some claim this next fix is BS, and others swear by their grave that it works. But run your RCA's and power wires at least 18" apart. I route my RCA's on one side of the car, and power on the other. Couldn't hurt.
This is already done as my RCA cables go to the amplifiers which are located on each side of the vehicle...the main power wire goes to the distribution block in the middle and also goes to its location across from the RCA's and not near, The two cables may cross each other at a location but thats about as much closeness as they get.
Grounding the RCA's on the head unit
Many have had problems with Pioneer head units because of a poor internal RCA ground. To remedy this, simply wrap wire around the RCA's and screw the wire down to the head unit's chassis like so:
Im pretty sure this isnt an issue.