Ok, so the issue is still present. We installed ground loop isolators to try to correct it and the noise still seems to be there, it's better (at least I think it is) but there. This problem started happening once the Avic-D3 headunit was installed and I never had the issue with the OEM headunit.
Also, the noise DOES seem to get louder when I accelerate, unlike what my initial post says. It is not however coming from the engine.
Any help would be much appreciated. My installer is stumped as well. He told me not to worry about paying for anything until we fix the problem.