I managed to snag a Long Club from a wild Cubone using Thief, which worked just fine. Not sure about the Moon Stones, but just to confirm Thief seems to be working. 🙂
This is really cool! It works for Pikachu when I add a 025FCry to the "cries" folder. However, whenever a Pokémon that doesn't have a special faint cry faints, no cry is played at all. Was this intentional?
I'm fairly sure the Starter Selection script by Limnodromus has a method around forms. I don't know what it does exactly but looking there might be the right direction.