I guessed I'd need a 3D program to do it, I even tried opening the .obj files I exported in Photoshop but instantly knew that wasn't the answer. I downloaded Blender, a free 3D package that was talked about elsewhere on Subsim but haven't even installed it yet so don't know if I'd have solved my problem with that, I know I can't afford 3DSMax, lol, especially as I only need it for this small task, I guess the trial would have done but at over 3gigs, it's a bit of a heavyweight, download-wise.
FM, you would be doing me a great service if you help out and is a great example of how people in this community are so willing to help out people with dumb questions, LOL. When you say you are going to upload the corrected maps, do you mean I can just use the import option in the 3D Model options to apply it and it's sorted? Also, the engine room, quarters, and radio room have their own geometries for the lights separate to the CR. Asking you to map all those sections is too much so please let me know if Blender will do it, and maybe I can get it done. As it is, the difference between the CT bulbs and the rest of the boat isn't noticeable as much as not many people spend their time sitting in the CT, but add the textures to the CR and not the rest of the interior, it becomes glaringly obvious.
I've just uploaded a beta version to filefront in preparation to distribute to the people that need to see it before I release fully, but I did it with a heavy heart as to me it was unfinished without those bulb textures. If you want me to PM you the link to my mod as it is now, just say and I'll PM you, otherwise I'll wait until I get, in my mind, a finished article.
Thanks again for taking the time to help the best you can, you're a legend.