Yeah...as I recall, the guidelines forbid time-travel tales.
However...you've got a good idea. A nice "high-concept", as it were.
Myself, I'm writing a Trek novel, too--one that violates the guidelines, BTW.
The thing about the guidelines, though, is that they only apply to rookies. Once you're experienced, you're free to try and publish this one.
Now...I wrote a plot synopsis first. I then left it alone for a while--long enough for me to get new ideas to work into the tale. Then, I re-wrote some of the plot.
Finally, I started writing.
As for where to start. Ever heard it said, "Start in the Middle"?
That's bunk. You wanna start at the beginning
of the plot--or a little bit before. Still...start with something that will pull the reader in.
Something emotionally relevent to the story...but with an undertone of "Hey, something interesting is going to happen."
When you write, use the synopsis, but take care--it's not carved in stone. If a new idea hits you (a new scene, or a new plot turn, whatever), by all means write it!
I would use the guideline as your basic agenda
--the general idea for your story. If you're stuck, refer to it. It'll help put you back on track.