A few quick things:

You said you used "2 (cheap) two-channel speaker-level to line-level converters" to hook the Pioneer head unit to the Element's factory amplifier.

Questions about that:
1. Are you sure the Element's factory amplifier is really line-level input?
2. Do these cheap converters have power connections or are they passive?

If they have power connections, they could be causing the ground loops.

If the Element's factory amplifier is truly a line-level input device, have you tried connecting the empeg DIRECTLY to it without involving the Pioneer headunit or any other converters or components at all? Remember the simpler the layout, the less chance of ground loops.

Why do you want the Pioneer stereo anyway? If it's just so you can play CDs, forget it. You'll never play CDs again anyway.

Final question: Why did you buy the ugliest car on the face of the planet?