One last question, I notice that whenever I attack my NPCs they don't initiate combat with me, so I can kill them without any resistance. I know there's a function call CharacterAttackCharacter, but I assumed they would at least defend themselves.
I then noticed that the editor kept saying my NPCs didn't have any alignment. At first I thought it meant their spacial alignment, but now I think it talks about whether they're good or bad. Could this be the reason why they aren't attacking me? What alignment should I set for them? Will this affect being detected while picking pockets?
Yes it is. Try giving them CYS_Village as an alignment. Or Evil NPC (no underscore).
If that doesn't work you need the Alignments.lsx file from the same templates folder as before. It goes in Data\Mods\YOUR MOD/Story/Alignments
This is one of those things Larian should have made automatically copy but never did for reasons.
One other random tip about the dialog checks. If you are using level override to make your character level 5 for testing, it does all sorts of goofy stuff with skill checks. So if you're testing those make sure you're at the default level override.