Re: relocated battery. Now getting whine though stereo
running your rcas and power wire down opposite sides is unnecessary. Maybe back in the early days of car audio you needed to do it, but with todays noise rejecting RCA's and higher voltage pre-out decks, you just don't have to do it. This is assuming you haven't used $3 Walmart RCA's of course.
I've been an installer for over 5 years now and in that time I have run the power, speaker wires and RCA's all together countless times. Guess how many times I've had alternator whine because of it? 0 times. NEVER.
Alternator whine is usually caused when you have a ground loop. Measure the resistance from your battery ground to your various grounds in the vehicle (amp, head unit, etc.) they should all be under .2 ohms or less. If you have one that is higher than the others it's bad and is likely causing the noise.
In my experience, 90% of all engine whine is caused by a bad ground. A ground loop isolator should be a last ditch band-aid if all else fails.
Also, just an afterthought, but what condition is your battery and it's connectors/cables in? If you have a dying battery, it cannot effectively filter out the AC ripple from your alternator and will cause noise. If you have a loose or corroded connector you will get a high electrical resistance and it will cause noise.
Good luck.