I also have a Porsche Boxster (2001 S) and have the same problems...

The Empeg isn't the source of the noise; I can disconnect it from the head unit and the AUX input on that unit will display the same problems. The FM doesn't seem to suffer it though.

While I concur that a good grounding is an excellent idea, and I just might try using some CAT5 for interconnects, I think the AUX input of the Becker factory radio just blows goats.

If you make any progress in solving these problems, please do let me know, and I'll do likewise.