This sounds absolutely amazing to be a part of. Being able to give ships a proper shakedown and with enough people doing various aspects of gameplay this should really help to dial in ship stats, strengths and weaknesses.
I would really suggest a proper shakedown cruise map either Cryptic made or Foundry made that puts a ship through all the typical, maneuvering, light combat, heavy combat and fleet combat.
The fleet combat being a variation of the 20 man PVE, the other 19 being allied npc vs a few waves of different enemies. 1) Orions, Nausicans, Hirogen 2) Klingons, Feds, Romulans. 3) Cardassians, Elachi 4) Undine and Borg.