After extensive testing with the shadowkeeper I have come up with the following advice.
Be very careful when changing a characters class alltogether. Changing their class can very well "unflag" them, making them in essence scripted PCs that can't activate their personal quests. Minsc and Airie are highly editable since they don't have any personal quests that can screw up. Keep the changes moderate on all else.
Kits are sometimes troublesome to add since the NPCs never have been one level "0", hence they miss the level 1 benefits of the kit wich sometimes can not be duplicated.
Proficiensies, spells and skills are all completely editable without fear of screwing something up as is the animations safe to alter.
When editing an NPC fundamentally by changing it's class it's a good idea to just drop the level down to 1, erase current skills and spells, add the skills they should have, change their hp to the equivalent of a first level character of that class as well as the profiency slots. The load the game and let the character level up to it's current experience points. Thac0, saving throws and spell memorisation will alter itself so you need not bother about that. Beware that this is very likely to alter something in the scripting of the NPC wich, when it's the worst, completely strips the NPC of all it's quests and dialogues.
So be moderate in your changes or be prepared to gamble. Giving Nalia a speciality as a mage is completely safe compared to altering her class to a monk wich in my first time around made her unable to grant me the keep as a stronghold. The second time it worked without problem though so keep making those back up saves just in case. Other trouble that might occur is that since the NPCs miss level "0" then the game might think that they are at one level below the one they actually are. This is also not always true and depends quite a lot on what class and kit you altered the character to.
That's all the general advice I can give to you. If you have more specific questions I'd be happy to answer them.