What did you end up doing with the stereo? Do you have the FM Modulation installed for your iPod? Still using the factory head and amp?

The fix for the hatch mentioned is only temporary. The tape will wear out. There are adjustable feet that are intended to take care of a loose hatch. I adjusted the "feet" to press a tad harder on the car body and the rattle is gone.

With regard to the noise you just wrote about - sounds like amp noise, probably from radio interference or loose wiring. Source depends on what you did to the stereo and whether or not that is the cause.