I chose to cut this Gordian knot by remaking the base ship using a looser loft instead of normal loft. Evidently that must have cured the wacky fold that you pointed out.
Hey Yenmonger,
I looked at making this shape a little better with a "rail revolve".. Here is the result.. The revolve curve I had adjusted the 2 endpoints to be tangent, as opposed to the little wiggle at the end. I also made all curves planar.