please think outside that damn box and offer any oddball solution you can think of!!

Start over. Get a lot of extra wires from the store. Yank all of your components (down to but not including the existing wire runs or the speakers). Bring the components into the car and lay them on the seat, making sure nothing touches metal. Use lamp cord, speaker wire, whatever and make all power and ground connections directly to the battery. Let the cord go through the window (or whatever you do with a convertible). Also use the battery to supply turn-on lead (just make sure to disconnect it if you go in for the night). Run short RCA cables to connect the parts. Again do not use any wires already in the car, only new stuff. Just like you would if you had no car, but instead only had a workbench and a spare battery.

Fire up the car. You should have no whine. If you do, you can be guaranteed that a component is bad, and you're simply screwed. Invest in a better amp / cd player, or another empeg. If there is no whine (not just faint, but none at all), then you have succeeded. Now you know that it was your installation. Put things back one by one. For example do not put the whole empeg back at once, but do it wire wire, connection by connection. Fire up the car between every solder you make. The inside of the car will look like a mess, but that's fine for now. Wire nuts are your friend for temporary fixes.

Eventually, one piece at a time, you'll get almost to the current setup, and the whine will be back. The connection that brought it back will be the source of your problem. Fix it.

Sounds like a real pain in the ass, but it will solve it. It would take less time than continuing to tinker with it. My opinion is that anything else you do is pissing in the wind and wasting time. Eventually you'll get lucky, give up, or realize that if you had pulled it all out you'd be done by now, but without the alternator whine.

My $.02 since it's what I'd have done a long time ago.