U.S. amps are located in the left rear quarter panel along with the cd changer. I can't really think of any reason why tapping into a post-amplified signal could have any effect on the preamp section, especially causing it to turn off...

Noise that becomes amplified after the signal or ground shield makes contact is typically caused by what is called a ground loop. All this essentially means is that there is a significant difference in resistance (impedance) between the ground for the source unit and the ground for the amplifier. Countless times I have seen this to be a product of cheap electronics with worthless internal filtering. You could use a ground loop isolator, but you should have power to spare because it will reduce your signal input. Additionally, it is odd that your are getting induced noise through your subwoofer. Does your amp have a low-pass crossover? Induced noise is often in the frequency range much higher that 20-100Hz that is the typical range of a subwoofer.

You may also want to try a different location for your amplifier ground. If it is not a very good one, the amp will try to pull a ground through the RCAs, which is not in the design of any of the components.

1) Try a new ground first, make sure that you have scraped away the paint that is on the chassis, so that you can make a clean metal to metal connection. (Make sure that you are not putting a screw into gas tank or brake lines etc!)

2) Try to ground the RCA outer shield on the amplifier with inputs plugged in.

3) Last resort, try a ground loop isolator or replace your head unit with an aftermarket one. This would be my vote since it is easy, and you can gain bluetooth handsfree, ipod link, dedicated preamp outputs, satellite or HD radio etc. etc. This is simple since you can just wire up a basic harness and feed the factory amp a high level signal. The only downside to that is if you have a weak sub amp and you can't turn your deck up very high, it throws the ratio off and is tough to get much bass.

Hope this helps