Nine times out of ten, alternator whine is caused by the power wire touching the rca's. In your case, you did good by running the rca's down the passenger's side of the car. The driver's side usually contains the power wires for the electrical in the rear of the vehicle, which can lead to noise.
I would double check the routing of your wires. I'd be willing to bet that your rca's and power wire are touching just before they enter the amplifier. This is a common problem when installing systems, since some amplfiers put the rca's on the left side.
If that isn't the case, swing by your local Circuit City (keep in mind, that's where I work) and pick up a ground loop isolator. This piece just might be the answer you are looking for. They don't always work, but may be worth a shot.
Good luck to you and let me know if I can be of further assistance.
