So having played the first two missions through, I would like to say that you have done a great job capturing the TOS flavor - kudos on that point.
At the same time, I am hoping that you aren't going to follow too much in TNG Season 1 footsteps and just grab a random episode and re-visit it for each mission. While I understand that there needs to be some nostalgic stuff to grab players and make them feel like they are in the setting, there's also a reason why TNG's first couple of years are generally considered the weakest, and its because they fell into the trap of doing too much of this and not enough new stuff.
From a personal perspective, I want to feel like I am exploring new territory, not following Kirk around and cleaning up his messes. Other will likely disagree, but I would like to just put that out there.