Does the loud-noise-that-fades-out happen when the RCA's are disconnected from the amplifier?

If so, that would also lend credence to the "faulty amplifier" theory. The only other thing I can think of is something really screwy with the wiring, like the headlight illumination wire plugged into the amp remote line or something like that.

But you're right in that most kinds of ground loop noise would simply stay constant with the engine running, and the "fades out after a minute" would make it sound like it's not a ground loop issue.

Except for one particular situation where I know the empeg will make a high pitched whine. That's if you are listening to the AM radio on a certain frequency. My tuner module makes a high pitched whine on a certain AM radio frequency when the unit is cold. As the unit warms up, the whine goes away. I even made Hugo personally witness this one, just to get corroboration. But I don't think this is what you're talking about, right?