Shielding in car audio interconnect helps to pick up EMI. Be careful what interconnect you use. There is such a thing as crappy simple cable that is more susceptible to noise than others, but you may also be running it too close to your amp's power wire (though, really, the car's entire body is a ground that could also be a source of noise to your wire. :) I'm actually running cat5e UTP as interconnect. One run is good for two stereo pairs.

Do you get any noise on any other components? Where did you ground the empeg? If you thought the +12 wire in your dash was bad, you should really think about grounding the empeg (and your head unit) directly to the chasis as well. Bad grounds are a common (very common) source of noise in car audio. If you're grounding to the chasis, use an existing bolt if possible. Do not expect a good ground through the actual bolt. You should sand/gring the paint on the chasis where the bolt attached and make sure your ground connection touches bare metal. The bolt is just there to hold it in place (same goes for the ground connection for your amp(s) in the rear - but in that case you should have a dedicaed bolt, right through the floor of the vehicle).

It shouldn't be a big deal to run a new +12v 18ga into the car from the battery. Find where your current amp line comes in and put the new 18ga wire through the same grommet. Look under your dash so you know wher the wire will come through and then use something like a wire coat hanger.

Off the fuse panel you might have to unmount the panel so you can access the wiring on the back. Wire it into something suitable of course (ie. not protected by a fuse rated too low, provides constant 12v, etc.) Depending on your panel selection, it might be a better idea to go to the battery.

You're likely only having a problem with the stock wiring because of the drain your Sony HU's amp puts on that line. The same type of thing you see when you're using a line from your amp wiring and you get a good bass hit (though the fact this is hapening in this instance actually surprises me). You may end up with the same problem even when going directly to the battery if your amps are sucking too much juice on those hits. If that's the case then you'll want to go with a cap wired in parallel at your amplifiers.

Bruno