Did you read the FOMOD? It says CHOOSE TO DISABLE which means when you're clicking on each NPC in the installer, you're disabling them, not the other way round.
Reinstalling the mod over the top won't do anything because you've already moved the script that disables each of them into the game directory. Either you need to go into your Data/Scripts folder manually and remove it, or do a clean reinstall of the mod and only tick the option for NPCs you don't want to appear in the game.