Before S6, I was playing around in the Foundry trying to set up an interior of a ship along with some maps that could be used for RP, but unfortunately Foundry is down at the moment, so I haven't had a chance to dabble further with that.
I've been active in email RPs (or sims, as we call them) for about 10 years and have run a few of them, so I have some experience in storytelling and setting in that regard.
Getorix's roster layout is what I'm used to as well, so I think that would work great. DoctorDisaster's are also very valid and are good to think about before we decide what to do.
Perhaps, instead of basing it on a ship exclusively, we could base it off Stonewall Starbase and have a ship attached to it that isn't necessarily under the command of a specific person but is commanded as mission require it. Somewhat like the Defiant for DS9. That way if we choose a captain for the RP who isn't available for a session, someone else can easily run the mission. Also, since RP is mostly ground map based (if we're playing as a crew), it gives us greater scope.
The key, I've found, is to be flexible, so that if someone can't be part of the session or new people join, they can easily be fitted into the RP. New people or rotating crew can just come from the base. It should be more important to have fun than to keep everything super strictly in fitting with canon or storylines, in my opinion. We all have different playing styles, after all.
As for characters, it's probably best to stick to your toon's career division if they're an officer, ie. Science = Science/Medical Department, Tactical = Security/Tactical Department, Engineer = Operations/Engineer Department. Civilian positions won't matter as much, obviously. :)
I'd suggest using the Fleet uniform as our RP uniform, but if we choose another one, the extra uniform slot - or "off duty" slot - could be used for that. Since you can basically completely redesign your character in it, it's rather useful. Although, if we want to use off-duty outfits in the RP as well, that might not work. :)
My main character is a Human Male Engineer and my two alts are a Human Female Scientist and an Andorian Male Tactician. So basically I can fit in anywhere, really.