rather than checking every square inch of speaker wire or RCA wire simply disconnect one speaker wire at a time from the amp... did the hum stop? disconnect one then the other RCA did the hum go away? A RCA that has been pinched during install or in a door jam can also make the cable susceptible to alternator whine (I make some of my own RCA's and I did a lousy solder job and that gave me intermittent whine)

I had multiple grounds last time and it was a pain.

substitute the HU with a portable CD player (with the old HU removed or at least off) that should tell you if it is the HU

 

i would undo the speakers form the amp
then a new pace of wire to a speaker ,do all speakers ,if you have a wine you know it is the rca or a ground thing
then run a new rca wire to the amp (if you have a wine then you know it is a ground)

 

Just ground the damn preouts of the deck...sound will go away and you will know its the deck.