CBS is the rights holder for Star Trek. And dealing with the top people in CBS, I can tell you they are decent, passionate people who love Star Trek. Already we are at an advantage. They are not trying to screw with fan films. I have had serious discussions with them and they honestly would love to work even more with fan films, but because Paramount owns the movie rights, the situation is very tricky and they simply cannot do anything.
Mallory is the legal person who looks after the fan film community, and while I haven't spoken with her, I have heard nothing but great things about her from Phase II and Secret Voyage. She will tell you what you have to change to fly under the radar and she is very helpful.
I will get contact info for her and chat with her how she might want inquiries to go.