First thing, are you using a Mk2 or a RioCar? If it's a Mk2 you may still have the Rolloff caps installed near the RCA connectors. I have now had 4 customers say that their "alternator noise" in BMW, Audi and VW has gone away after I removed them.

Secondly, have you tried earthing the cage of the player to the same earth point as the amps and the player? If not, and by earthing it the sound goes away, then you have got an earthing problem with your empeg, probably not grounded at the same spot as your amps, and without a sufficiently good ground (paint not scraped away?).

Thirdly, what gauge wire are you using for the earth wire? (This should be EXCESSIVELY large).

Fourth - are you sure you have connected the "Memory" feed from your car to the empeg harness permanent power feed, and not switched it with the ignition sense?

I am not always sure that people describe the noises they hear properly - does the noise you are hearing rise or fall with engine speed, or is it constant? Does it disappear if you stop the car and turn the engine off? Is it high-pitched, or low-pitched? Are there any other noises you can hear, say when you press the brakes/turn on the wipers/turn on the rear heater element/etc.? This would give symptoms of poor suppression in your installation, so it might be worth finding power filters for your amps.