Don't know enough about the issues, or the cowl shape you're trying to achieve. I've used MicroStation 3D surface modeling before the Bentleys wrote it - when it was Intergraph IGDS CAD. My experience has been to stay away from the b-splines. They're convenient to get an odd shape, but they don't convert well - if at all. Maybe that means my experience is a lot less than yours, though.

Oh - by the way - my MicroStation is only SE, but I'm not sure the J version contained any additional functionality for 3D.