tbh, i've never found interferance to be an issue with having power cables near rca's or speaker cable, saying this, i've got my power running up the passenger side and all my rca's and speaker cable running down the transmission tunnel (i cut a section of carpet out under the centre console for it all to pop out of) it's when it reaches the boot that they all start to get a little close. i have speaker cable touching the power and while it's technically not the best thing to do, in my case i've noticed nothing in the way of interferance.
in my experience engine whine is either a bad earth (have you stripped all the paint back from the earth point for a good connection?), whether it be the headunit or the amps earth so i'd check them first, or, if you've got passive xovers the positioning of these can cause problems, i shoved mine right near the fusebox and had constant clicking until i realised what was making the noise.
Another cause could be a knackered alternator, if it's on it's way out it can intrduce noise into the system.
as for earth points, you could strip the paint back from the screw that holds the sparewheel in place and use a nut of the right size to clamp it down before putting the spare wheel back in, or anywhere else that is reasonably substantial that you don't mind takingthe paint off,
hope some of this helps mate, i't a pain when you get noise in the system, but normally it's something simple like ther earth point
