I've done some more testing this time, and so far my changes have been successful in what I've aimed for so far... but I'm not there just yet.
The prologue at this point does what I wanted it to do, the enemies now can't completely kill Eirika in one shot, but they can do serious damage to her.
The prologue and Chapter 1 are somewhat easy, Eirika can do virtually all the work if you so choose (though to be honest, in my hack, Eirika actually is pretty good), but Chapter 2 is where the change becomes noticeable. What I did is give the bandits higher HP and STR, (though I'm starting to think about changing the generic bandits from low hit rates and the ability to instantly kill most of the team to higher hit rates but slightly less damage), and the boss of the chapter is noticeably stronger. What I'm considering is that the enemies should all be given less damage and a higher hit rate, because as it stands right now I feel like the difficulty isn't 100% there yet. Chapter 3 is relatively easy, except for the boss who is ridiculously strong. Like, borderline Gomes strong for this point in the game. This is another problem which I intend to fix, because as much as I'm shooting for a difficulty up there with the likes of Thracia 776, early bosses that are beatable only by prepromotes are not what I want for the game.
To make a long story short, the game, while working so far, is not quite where I want it to be.
I'm going to start on the more complex aspects of hacking at this point, and it's anybody's guess as to how long it will take. To be quite frank, I'm going into (mostly) unknown territory. I'm going to try and make this as good as I possibly can, and I want everyone to keep the input coming, it's really been a big help to me so far.
Oh, and by the way, L'Arachel has been the subject of some favoritism. At this point I'm not sure if anyone is surprised, but yeah, I was totally going to do it.