2. i have no idea- are the two groups named uniquely, and are your textures uncompressed targas/DXT1-5 DDS's?
3. there's no tutorial - just remember to select 'float array' as your edit mode,
opacity can be changed by opening the 'Oc' node in the .mat and editing the float value, 1.000000 is opaque and 0.000000 is totally transparent.
btw, if you're concerned about the polycount impacting game performance, you can reduce it quickly with the DirectX Mesh Tool, simply drag the slider to the left and when you have the desired polycount click the save work button. then export this lower poly model as lod1, (cmp exporter version 0.3!) and add another LOD range to your INI. 0, # is the range your Lod0 is displayed in- #, # the next(Lod1) and so on. low polycount gets less noticeable the farther away you are, and at 10k (SP/Dev's limit breaking hacks only) every small ship is just a few pixels or less. i'd recommend using a range setup like 0, 1000, 5000 with full polys at less than 1k, and half that beyond 1k - of course all this depends on the size of the model, and polycount - a high poly capital ship model in the 5000-7000 range usually has four LODs or more.
getting farther off topic, using the new LOD capabilities in the exporter and the multiple-mesh export you can make a ship with ten thousand polys and a scale-mile long that will only display a quarter or less of those polygons at near distances - because the engine is smart enough to use the given LODranges on a per-part basis, meaning that a 5000 poly part on the other side of the ship will render a lower LOD(and less polys) than the same part on the near side, if it's setup properly of course.