Yeah I'm completely open with the story, what's on the wiki right now are just placeholders more then anything. If you want, make a new page on the wiki and add all your ideas there, just make sure you link it somewhere visible (here, on the ideas page, wherever really). I'm now going to focusing on getting all the pending team ships modeled so that will be one step towards having everything needed to get the story going.
Git is a pain in the ass, to clone through HTTP you need to do a shallow clone and set the download buffer to a stupidly high amount. Shallow cloning only clones the latest commit on the repository, I had to do it when cloning SSGX otherwise it would just refuse to clone and kill itself.
I'll send you a PM outlining where everything is and what it does. I think implanting a controls menu is a good idea, you'll need a third party input manager though because Unity's default one only allows you to change the controls when the game isn't running (it reads the controls from the registry on launch and then forgets about it)