Changing initial party at start(2 soldiers and Terra)

I got you there, this character in question isn't going to be permanent(in fact, this character is the main bad guy) the girl character I have replacing Kekfa will leave after the boss fight, so it will be a guest character. My only concern is that I don't want to have a bunch of soldier sprites looking like the girl that I have replacing Kefka later in the game.

These are writing to character slots $0E and $0F, so as long as you keep the event where those 2 characters are removed, you're fine. When you assign graphics to a character, you aren't changing the graphics for any NPCs. You are only affecting a single character slot.

Note that other than the main characters, only a handful of spritesheets have battle sprites, and the vast majority of those lack character portraits and/or the ability to ride chocobos and magitek:
Soldier - has portrait AND riding sprites
Imp - has portrait AND riding sprites

Banon - has portrait, but no riding sprites
Leo - has portrait, but no riding sprites
Ghost - has portrait, but no riding sprites

Merchant - no portrait or riding sprites
Esper Terra - no portrait or riding sprites
Kefka - no portrait or riding sprites

My patch "Everybody Gets a Chocobo" gives riding sprites to everyone except Kefka. I have not made a patch that adds portraits as of yet.