Did you reuse the negative from the wiring loom for the headunit? i usually ground the headunit to the metal inside the dash so i know its got a good connection. may be worth trying if its not your rcas as it doesnt take long and you will have the deck out while your swapping rcas anyway

Also if your rcas arnt damaged but are causing engine whine they could be run to close to other soruces of power(this can cause engine whine) so it may just be the rcas are poorly sheilded and/or run too close to other wires.