Hello! I downloaded your Atlantis City addon and read your forum. Some time ago I also tried to create an Atlantis for the orbiter. It was quite the obsession for me. I managed to make a working ship using a 3d model from scifimeshes and also add textures. Thou I didn't use spacecraft3, just a config file. It didn't have a gateroom or a jumperbay but at least the thrusters were working correctly 
I also tried to create a module but it didn't work correctly. Maybe I can send you my work. I think it would be much more useful to you. I'm not a programmer...
I also tried to create a module but it didn't work correctly. Maybe I can send you my work. I think it would be much more useful to you. I'm not a programmer...