Forget the empeg-specifics for now. You have a noise problem period at this point. I suggest you go to www.carsound.com and search around to see if anyone has posted concrete Boxter information. You'll have to wade through the noise on that forum unfortunately.

If you can get an aftermarket harness adapter for the Boxter factory connection you can more easily run tests that bypass the Becker unit completely. Then you can try running power directly to the battery, etc. to see if it has any effect.

I'd probably get rid of that Becker unit anyway, simply because it looks far too ghetto to installed in a decent looking car.

Bruno