Ok! I think I got it!
I copied the rank of ENS and renamed it XXX. The three ensigns/XXX stand watch, so I linked the new rank to a different and new uniform set. So those three officers on the conn watch rotations where unique uniforms!
All I have to do now is edit an officer hat with some scrambled eggs and add a commander rank and voila! Captain on the conn!
All that is left is to is make a new crewman3d.upc with the new uniform set and make all of the heads the same. I'll have too fool with that tomorrow.
EDIT: Well poo. The games crashes if I make a new entry [CrewMember3D 7] in th eupc. Back to the drawing board.
EDIT: I figured it out! I had to add an entry int the UPClocalization