In my experience those shadows can be sorted using Bryce's mesh edit tool - Its the furthest to the right on the Edit palette.  Pressing 'unsmooth' gives you the raw model, so to speak.  I find that adjusting the slider to 22 or 28 degrees will usually get an imported model how I want it to look. 

I've recently discovered that textures can be blended using the material editor which has led to me half UV mapping models, and blending with object cubic applied textures.  This is good for putting logos over panelling, and is how I textured the shuttle in my 'Golden Age' image.]

Nice ship btw - I only seem to be able to model small things.