Maybe the empeg is fine and your Miata sucks in this regard?

I'll suggest it again - unbolt, unhook, "unwire" every stereo part in your car and lay it out - the empeg on the dash, any amps etc. on the seat. Run temporary wires between them all. Don't re-use a single piece that's in the car at the moment. The car will look like you dumped spaghetti inside, but so be it. At this point, with all wires out in the open, use only the battery post for power (and a switch for turn-on) and ground. I'd be 99.9% sure you'll have no noise problems. If you do, you know a piece of equipment is faulty, otherwise you'll know it's the wiring job. Then put it back, wire by wire, replacing the temporary leads with what is installed already in the car. One of them will bring back the noise and you'll know what to work on.

I'm sure it's something simple - a signal wire too close to the heater blower motor, something grounded to a piece of metal which in turn isn't grounded to anything else, whatever it might be. You've worked on it so long that you're overlooking the problem, thinking some part of the installation is good, when in fact it is not.

I dunno, you've talked about it for ages, I can't believe you haven't just ripped it all out and started over.