Glad you got your problem fixed but just to clarify, the adding grounds was a last resort after all components and wires were checked as to not being the problem. Some people disregard quality RCAs but if you have decent hardware it just doesnt make sense to connect them with crappy wires. Just to add on the ground issue now that your noise issue is resolved, adding grounds or upgrading them will probably make it sound even better AND improve the efficiency of other electronic components in the vehicle.
I know this is an old post but I figured I would post my findings since I was successful in my final attempt to get rid of the alternator noise.
I never had to change any grounds at all.
I purchased a quality set of twisted sheilded RCA cables from Amazon and ran them down the left side of the car away from the power wire.
I also purchased the newest PAC audio harness PAC C2R-CHY4 from Amazon for 73 bucks.
After installing these 2 new devices to my Pioneer Z-2 and Kenwood amp, I had zero noise from the alternator.
One last minor change I made was to move the amp to the left side of the trunk storage compartment. Didn't know if this would help but I figured any bit would help.
Hope this helps anyone that has been dealing with it like I have been.