A few things:
1) Yes, get everything in writing. Despite being a lawyer, I trust people too much and often get screwed. I grew up in a time when my Dad taught me to do a deal with a handshake. But that no longer works. Everything needs to be in writing.
2) Getting a script done is more important than sets. If you have beautiful sets but no script, then your sets sit there costing you money.
3) ONLY build the sets you need. And you don't know that until you have a finished treatment.
4) Why build sets? Seriously, you have to ask that question. I know it is cool to have sets, but what is your goal? Is it to produce a great Star Trek fan film? Is that best achieved by building your own sets? Why not partner with another production that has sets? (that has its own issues of course). Excalibur is considering virtual sets. Just ask the question and have a great discussion about your goals.
5) Have a budget. Plan this out. Know what your costs are.
6) Have a timeline. Know how long each element will take. This also helps you with # 5.
Finally, when you guys have a script, David Gerrold, the writer of "The Trouble with Tribbles" who has directed for New Voyages is interested in chatting with you about directing. I spoke to him last month and told him about you guys.