Alright, a couple of things. It was right to have your spotlights on a separate render layer. However, you also need to put the ship on a separate render layer and set it on the spotlight layer so that the spotlight layer alpha is masked by the ship layer. It’s the little buttons just below the layer buttons in the layer panel. On top of that, your method for blurring was wayyyy too complicated and would only cause you headaches with different camera angles down the road. I completely rebuilt the compositing to reflect this. You can add on top of these settings whatever you’d like now.
In the world panel I saw that you had Ambient Occlusion settings set to 3 samples. This really doesn’t do anything visibly useful except greatly increase your render times. I went ahead and set this to one. You may want to consider lowering the error a bit, but for this scene it doesn’t appear to be necessary. I also always advise turning pixel cache on, as it is a huge time saver. I also turned on falloff to give a more physically plausible effect to the bounce lighting and AO.
The only other thing I did was I took the liberty of adding two spot lamps parented to the emitting objects to help sell the volumetric effect. This was just personal preference, feel free to do with this what you will haha.
I love the model, very cool. My only suggestion would be to change the emiting spheres to slightly convex lenses coming out of the front of the cowlings as it would help with the compositing effect from the side and help to lower your AO calculation times in the long run.
Anyway, let me know if you need any other help here. Happy Blending!
EDIT: Oh, one more thing! The reason adding lighting wasn’t working was because you were only adding it to one layer, the spotlight layer. You need to make sure that lamps are on all layers that you wish to use them on. You can do this by clicking your lamps, pressing ‘M’, and then shift clicking every layer you wish to be lit by that lamp. I also parented the camera to an empty for easier panning of the camera around the ship. If you find the camera isn’t behaving some way you’d like it to, this is probably why.