Probably not the best method and I know people are going to hate me for this but look into a ground loop isolator.

Specifically a Jensen CI-2RR Iso-Max. It's expensive but after months of troubleshooting my alt. whine issue, I said to hell with it and purchased the Jensen Transformer.

Never looked back since.

You can purchase through Part Express. If it doesn't work, I know they have an excellent return policy.