You've been given some of the details but I'll combine everything into one answer for you and fill in the blanks that were left.
The episode with the sailor being thrown overboard is the two-part or movie-length pilot episode. If shown on TV, it's usually done as two episodes. On the DVD, it's done as a roughly ninety minute show. The pilot episode was given the name - 'A New Life' referring to Harm having a new life as a lawyer after having to leave his career as a pilot.
In regard to thinking she was being given a hard time by everyone, she wasn't. She was liked by most people but she had a run-in with the CAG (guy in charge of all the plane department) who was the pilot she flew with and another pilot gave her a hard time after the incident that caused her run-in with the CAG. Another blonde, her roommate, had an ongoing rivalry with a male sailor over who could benchpress the most weight.
It's also possible that you're mixing up the pilot episode with the fifth episode of season 2, 'Crossing the Line.' That female sailor did think she was being given a hard time by pretty much everyone on board and reported the CAG for sexual harassment. The CAG in that episode is the same one as in the pilot episode. She was being given a hard time but she brought it on herself with her own poor attitude. She actually has hair closer to red but does look somewhat like the sailor that went overboard.
The last episode in season 1, called 'Skeleton Crew,' is where Harm gets arrested and as someone else said, the series changed networks at the end of season 1 and this episode isn't always aired and was originally supposed to be followed up with the first episode of season 2. Since that didn't happen, they ended up going back to this story in season 3, partly in flashbacks, as Harm tells the story to Mac and that he now knows who the murderer is. It's left to us to assume that somehow, Harm was cleared. It's believed that the same person who murdered her also raped her. The most likely reason for him being cleared would be that a test would prove Harm wasn't the rapist and therefore not the murderer. This episode also means Mac now understands Harm's strange reaction on meeting her for the first time.
Harm is getting a Distinguished Flying Cross from Clinton for saving the CAG's life near the end of the second part of the pilot episode. He was riding backseat to the CAG and they were fired on from the ground. The CAG was injured enough that he turned over control to Harm, in what, happily! was a modified plane that allowed it to be flown from the back seat.
Harm being a Lieutenant and then a Commander - well, in the first season, when they actually aired the episodes, they aired them in a different order than they were originally supposed to be and they've never changed the order since. The tenth episode, 'Boot' should have followed the thirteenth episode, 'Defensive Action.' That's why he goes back and forth but it's the only time, unless you count the 14th episode of season 6 where the actor fluffs his line and introduces himself as a Lieutenant Commander when his character has been a full Commander for more than a year and no one caught the slip!
The inconsistencies aren't an issue. For instance, in one episode, one character has a sister and about half a season later, she tells another character, 'If I had a sister...' But since the sister isn't important to the episode and never shows up, it doesn't matter. (I rationalise that for myself by saying the character had a younger sister and the actress was supposed to say if she had an 'older' sister or that the sister was really sister-in-law, in which case, she must have a brother that we never hear about. 😉)
If you've enjoyed what you've seen so far, it's definitely worth getting the box set. It's cheaper than buying individual seasons, if you can still do that. It's also sometimes better than watching the TV versions. I don't know if in America they cut out a section of one episode that they do in Australia but I was confused when I watched the episode on TV but when I watched the DVD I found that they'd cut part of a scene that would have made it clear what was going on.
I and many other people thoroughly enjoy the series and it's got me interested in law and related matters, such as protecting people's rights and international law, when and why you'd go to war... Not being American, I don't have the school teaching that would make me familiar with such things as the Constitution and I've spent a fair amount of time happily trawling the internet and learning about these things, all kicked off by JAG. I'm also sure I wouldn't have as clear an understanding as I do of China's island building or various other things that have been turning up in the news over the last year or so. Worth it, in my opinion.
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