1,3,4, and 5 - pretty much do what you prefer.
2. 50 shades started as Twilight Fanfic. When it became popular the author re-wrote it and removed all Twilight references before she took it to a publisher. You'd have to do pretty much the same thing with any Star Trek fanfic you write. Getting already released Star Trek fanfic published as
ST fiction would be pretty much impossible. And from what I understand, the publishers of Star Trek fiction only request spec work. For more info, ask this same question in the trek lit thread*. The trek authors on tbbs don't come into fanfic forum to avoid litigation issues.
*Do not discuss your stories/ideas in that forum.