Only just seen this, feel your pain mate. My Pioneer install by a pro was good, slight issue with the balance being the wrong way round, but they sorted that. After I fitted a reverse cam I ran the cabling past the my new amp (in the OEM space) and along the passenger door trim and round the footwell to the HU. Suffered from alternator whine immediately. After some trim removal and taping wires as far apart from each other as possible and earthing to a bolt somewhere else in the boot it just went away. If it's not the earth, which it probably is, it could be cross talk from another wire if the wiring has been done too or even behind the HU. Wish I'd known to try earthing it somewhere else to begin with, no one thing seemed to cure mine, just persistent tinkering. I'm hoping it doesn't come back in the winter when she sits at a higher RPM idle, once I'm going the exhaust hides a multitude of squeaks, whines and rattles.
As for getting the centre console back in snuggly, mine was a real PITA this weekend when I changed the iPhone cabling. There's a bird's nest back there and it just wouldn't cram in. In the end I cable tied some of the bigger lumps out the way behind the plastic bits which are behind the HU (wish I'd taken a pic now) and shoved some boxes off to the side, just fitted back in after that. I'm loathe to take it out ever again!