Well the command pod's finished and I've started on the edges and bottom of the main hull but I've reached something of an impasse. If I put the shadows around the base of the neck, they appear on all of the side surfaces around the ship.
That said, I can and will still complete the ship with the underside details and put the impulse exhaust exactly where it had been before. I've experimented with replacing the texture in gMax's Material Editor, but the sides were assigned all at once so, it didn't really gain me anything. FOAS appears to be prophetic, my lack of 3D editing skills can be frustrating. I am debating whether or not to just complete it as is and return to the problem at a later date or press on with it and learn how to un-wrap now.