The hum is definitely from the sub. And I never thought about it but the amp is bolted to the seat. So, it may be grounding to the wires inside the seat. Also, I forgot to say this earlier, every so often I hear something that literally sounds like welding. I never see anything sparks-wise. I don't know if it'll help, but I'm sure that it has something to do with it.
No I don't have the HU hooked up to to the same +12v source. I have it hooked up through the normal wiring harness. I didn't think having a different + source would make a difference since the problem is with a ground somewhere
As for the HU being sensitive, I don't think that's the case. I had this exact setup it my previous car (when it finally broke down I just moved it to the explorer). It didn't do this in the previous one. It's only happened since I switched.