I just finished my starship texturing tutorial and emailed it to you. I also just submitted it to sfc3files.
As for the a1, a2, etc. dummy objects, those are the damage points. When an enemy's weapon hits your ship, it hits at one of these points. The letters represent the six sides of the ship, and the weapon will hit on one of these three points at random. For example, if an enemy ship is behind and to the right of your ship and fires at you, the weapon will hit at either c1, c2, or c3. If the weapons hit the hull, these damage points determine where the damage textures appear on the model (assuming you have damage textures). To apply damage textures to a ship, all you need is a damaged version of each texture map and self illumination map with the same name as the original texture map or illumination map but with a capital D at the end of the name.