Look great, and I will absolutely use it.
Small nitpick/question... Are the Space Ports canon?
Can't remember seeing them before. A "mushroom" base would, at least to my mind, feel more right
The Large, Medium and small spaceports are from Star Trek: Enterprise - "The Expanse". Their just different views from the same station. The Gas and mining stations are from the Midas array. Resort base is a modified Jupiter station. I might change some of the stations to see if others fit the job better, but it looks nice ingame as is.
I can see the engines are located at the ends of the warp nacelles. I think it would look best if the engines were placed at the location of the impulse engines (none at all would be best but I don't know if that's possible). Usually the impulse engines are located at the rear of the saucer section on most federation designs.
I could put them there and see how it looks in game, or I might release a modified version for the people who don't want the engine effect. It might look a bit plain in game though, I could try changing the engine effects to something else and see how that goes.
So when you say your doing a mod does that mean like your gonna make all the neat star trek races out their & their ships 2?
Version 1 will just be U.F.P. and Starfleet ships & bases, as it progresses I will add more races.
Can you combine both your mods?
Yes that perfectly possible, I'm going to release this as a Customization Theme. So you'll have to copy the BSG ships into a race that hasnt been used yet for the Star Trek theme.