Final Fantasy Hacktics

Hey, this is probably a very stupid question but I went through and was just changing some existing generics in the storyline battles. Nothing major, swapping a knight to a dragoon, or a geomancer and some such.
In most of them, it seems fine, however in some it will cause certain units to become a blob of pixels. It is rarely the unit I edited, often some other random unit I may not have even touched, and it can even be the units I place from my formation.
I am not sure what is causing it. I just used the FFTPatcher to just edit their job class while leaving them as generic male or generic female. Anyone able to point me towards the issue so I can try and avoid it in the future?

I've changed some of the skillsets for some enemies for a custom encounter. I changed the loadout in their job skills a bit. For example like, I loaded Ja Magic with all healing/buffing. However I think I don't quite understand how to make sure they have it and use it. I set their jobs learned to 8 in the FFT patcher. I set the learn percent on all the moves to 100% and organize them from top to bottom by priority to learn.
Howeve,r in battle, they dont seem to have them or refuse to use them. They just spam haste over and over, or end their own turn.
Same with trying to give a summoner ONLY Bahamut, but with extended range and damage. He won't use it, even though he has the MP for it. He'll just close to melee and hit me with his staff. Even if I set his PA to 1, and take away a weapon, he'll still run up and try and melee me.
Am I missing something? I was under the impression if you just put certain skills in the skill set, and had the job thing set at 8 in the patcher, they'd just use everything in there.
What am I doing wrong?

I feel bad posting a second question so soon after my other one. I tried looking through an Event Editor to see if I could figure it out on my own by looking at the differences between events but I am a moron when it comes to this stuff.
Is it massively difficult to change an assassination mission to a defeat all? Specifically I am talking about the final battle series leading up to the end. Rofel, Kletian, and Balk.

I checked through tutorials and did some searches but couldn't find anything on this. Is it possible to change the battle theme that plays in certain locations? For example, is it possible to have the player walk into the random battles for a green dot and get The Pervert playing for a specific battle there?
Adding some hidden boss battles to the game, but would like to be able to give it music besides the random battle themes.