Yeah, sounds like you've got enough parts, and knowledge (and therefore I assume experience) to know the dentist drill sound when you hear it. You sir have alternator whine.

It's fishy to me that only the empeg does it. Your work in the car may be for nothing... you've done the light switch test and it says the empeg has done something bad. Why aren't you looking further at that? I think assuming the empeg is working fine, after another head unit didn't have the problem, is well, not a good place to start.

If this was my car (and know that I'm impatient), I'd rip every piece out and put it on the bench. Hook everything up like it is now, but just outside of the car. I'd probably use one power and one ground wire and just T off of it in a bunch of spots for the components. Make it play music and check for whine. If it's still there, you're done for, I'd call the empeg or the amp broken. If it's gone, that's great news. Put each piece in one at a time until it comes back. The whole ordeal involves a lot of extra wire and cables though of course. Me, I've done enough installs I have it all on hand though. For you there's probably a better way, but it's what I'd do. Especially at this point where I've tried everything else, and some things twice and three times.

One thing I'd try before I pulled it out - make sure the components are all powered and grounded directly to the battery, make sure none of them is touching a piece of metal themselves (directly or with a mounting screw), and make sure all RCA cables are not running alongside anything metal or any other wires. It's almost always worked for me. I've discovered amps that weren't grounded internally but instead grounded through their RCA cables, ground wires attached to large metal objects (such as dash frames) that in turn were actually insulated from the rest of the car, and so on. It's amazing.

Whatever it is, it'll surprise you, and you haven't thought of it yet. Time for something radical!