Also, since you know it changes with different items turned on / off (the A/C), be extra certain that the RCA cables leading from the empeg back to the amp aren't on or near any noise sources - as in, make sure the cables aren't running under the dash right next to the fan motor, as an example.

That would be my personal first shot - maybe even take the empeg out slightly and connect another set of patchcords (something from a VCR would even work) drooped over the seats right to the amp itself. See if the new path stops the noise.

Second, I'd check the ground point itself. There's been at least twice I can remember where I grounded to a metal object in the car, that turned out not to be a ground... Make sure you're grounded to the chassis of the car directly, and that you use a star washer or some other method to make metal to metal contact.

After that - if there's still noise, definitely go through the FAQ step by step.