first things first: woa
WOOOOAAAA AHA AHA oh thats nice so so nice.
and yes geoset animations can color specific vertex groups. its kind of like recoloring units in the unit data editor, only for special parts of models, and not just the entire thing, just find that skulls geoset, find the geoset animation using that geoset in magos, if there isn't one make one for it, then tick the ''use color'' check box, and then open the color window and pick the color you desire, the skull texture is white, so using geoset animations to color it is easy, if you'd like I can do it for you =D
Look forward to seeing that thing up close
edit: oh you did it already aha this one should be uploaded on its own truly. =)
edit 2: why, I wonder, did you use the lordaeron water texture? why not the uber teal blue sunken ruins water? (permission to make that change?)