brash_stryker, I use Apple Motion for any videos I make, and the standard colouring that comes with it, I do have Magic Bullet but I still go back to Apple standard.
Have you thought of duplicating your layers and creating masks for them, ie: bottom layer has been recoloured with your overall new colour scheme, higher layer is a mask of Jangos blue part of his helmet recoloured rust.....it does require time spent keyframing.....but does look effective.
Maybe you've tried this?!
J