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

That would be step one in the Crutchfield noise diagnosing flow chart that the FAQ links to. Yes I did.

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?

Nope, tuner is currenty working just fine, after a wire came out of harness #2 (like I said, greater forces seem to be working against me having an empeg, even more so than my posessed little car) which I managed to fix without any soddering.

Speaking of the tuner, I would like a pointer to some sort of tuner FAQ that can show me how to set up presets and stuff of that sort.

Now that I think about it, another thing that might cause that kind of noise is some kind of a fault in the wiring that runs to the speakers. For instance, the speakers accidentally getting wired as if they were bridged across channels that weren't meant to be bridged, or if one of the speaker wires contacted a ground or a power source, or something strange like that...

Nope, even went so far as to wire a completely different speaker with a new wire that was not attached to the car and got the same screeching. Now I'm really pissed that I have to dismantle this thing and endure silence for a while, unless I go with my friends scamming best buy idea.