the fuse box is one the the noisiest(electronically) places in ur car u should definately move it to the back of the stereo or the cigarette light which is where i have mine hooked up...also which speakers is the whining coming from? do u have stock speakers? or perhaps aftermarket tweets? and do u have an amp running the speakers?

 

i suggest making it super easy and just running a switch from your power wire on your deck to your amp(s)... have the switch in your console or something, just try different things

 

check to make sure you have resistor spark plugs. I know you can get a whine from not having the right plugs. I agree with the other guys....Make sure your power wire is run as far away from you RCA cables as possible. Too close will definetly cause engine noise. Just my 2 cents.

 

is your remote wire running along w/ your power wire?
mine did this too till i moved it w/ my rca's

 

If youve checked out the ground and rca scenario, have your battery tested assumming your terminals are making excellent contact. Low voltage can also induce alternator noise into a system.