After relocating my batter to the trunk I have engine noise coming through the stereo. However, the noise is only there if the A/C or
fan is on. Further, the noise is only audible at about 3.5K RPM & above. The noise does increase in frequency with RPM and it is present in every gear. I have the noise whether the radio or any other accessories are on or off; as long as the A/C is on. I do not
have any engine whine coming through the speakers with just the radio
or any other combination of accessories on (minus the A/C).

Here's what I have in the car:
Optima Red Top in trunk
2 2gauge Monster Power wires each for ground and power
Ground wires connect inside the trunk, above the frame rail to bare metal (all paint removed) with a star washer in the mix (common ground)
Stock Alternator for a 97SE
Stock BOSE stereo
I have every available accessory with the exception of heated seats (who needs em in Tucson, AZ???)

I have connected and disconnected the stock factory ground in the
engine bay with no effect. As best as I can tell, I am not in
proximity to any of the speaker wires or amps for the stereo.
I disconnected and cleaned the ground connections near the alternator.

For now, I am baffled!

Should I focus more on the ground connections or on the positive cable(s)?