I installed both the full install and patch. I followed the readmes to the letter. but when i load the star trek mod it gets past loading the XML and starts on the engine and i get this error:

GFC Error: failed to initialize the primary control theme

I don't know what to do....
any suggestions would be much appreciated.

Let me guess: you deleted the Final Frontier mod. For 3.0 I'll be including the theme in with the mod, but for now, just create a Final Frontier directory in Mods, download MOO2Civ (or any other Final Frontier-based mod) and take it's resource directory and place it in the newly created folder.

Thanks, I had the same issue. It might be advisable to mention this additionally in the installation guide :)