Ok, welll, I tried removing the tails on the saucer sep and placing them on the main body, but then that looked wierd, so then I tried removing the extrusion of the hull from the top of the saucer, placing that back on the main hull as well. That looked odd too.
Finally I just decided to abandon the sep for now. I have the Ares as a sep ship, and I will leave this as one piece for the time being, finish the textures and release it, and then revisit the sep idea at a later date.