You've done some good isolation efforts so far, I agree with the previous post that you're dealing with a 'logic box' somewhere. Since this model vehicle is most certainly a computer controlled transmission, and you can change the characteristics of the noise by switching to neutral, you're on to figuring out where the noise is coming from. I would start with basic bonding of the transmission housing itself, and perhaps some clamp on ferrites around any control cables exiting the transmission. Since it's so quick to move the ferrites around, trial and error with different cable harnesses is quick and painless to try.
Mark K5LXP
Albuquerque, NM
k5lxp@arrl.net