Like Joe sez.... I'd seriously look at the ground. Try to make a good
contact with the chassis of the car. I'd grind away the paint where the amp
grounds out to the car.
Okay, so your friend has an amp driving the 6x9s and only alternator whine
coming through and no music? Look back at the amp and make sure the
interconnects are hooked up properly to the amp and the back of the
headunit. If the amp is turning on but no music coming through and the amp
is only amplifying the noise I'd seriously look at that.
Again, inspect all wiring.
I got a question for Joe as well. Why would there be a LAG in the time the
amp turns off and the headunit turning off? If the amp turn-on signal is no
longer being fed into the amp, shouldn't the amp turn off immediately? I did
a trial install of my Pioneer GMX-944 amp and never had such problems.
Sounds like a internal design problem with the amp instead of a installation
problem. I know some amps have capacitors in the power supply to be used as
"reserve" when the bass hits. Maybe its those caps discharging through to
the speakers?
I'm just taking a stab in the dark here. Its about the only reason I can
think of why you would get a thud as the speaker is turned off.
Ken