Well, for one, I'd worry more about dropping the polygon count before UV mapping it. It would allow the UV mapping procedure to be far more easier and will save performance. Your pictures reveal a polycount of over 200,000 which is, in my book,'reserved' only for large warships with detail. With something as small as a fighter, you'll want to keep polygons at less than 10'000. Reasons for this is that fighters are generally placed in bulk during missions, such as squadrons and wings; and the detail placed upon them is generally unidentifiable at even the closest of ranges.
3 wings of highly detailed, 200k polygon fighters would heavily strain both your PC and the Freespace 2 engine, or may even crash them both altogether.
My advice is to do what I did with Tan.j's Battlestars; reduce polygons to an acceptable standard for the engine and fix the model in places it requires. You will also be able to identify places that can do without detail and learn techniques that will help your modelling in the future. I learnt more from trying to convert high-poly models than I did from creating them.
That's my advice on the issue.
P.S, for a lazy way of UV mapping a blender model, select it all in edit mode--hit space and type 'Smart UV map', its a cheats way I use when playtesting models to see if they hold up to performance standards.