Something tells me that you're trying to do this manually. Did you allow step 1 to do its job? You should've ended up with only 30 folders when step 1 was done with extracting Toon Link's texture parts.
Wait, THIRTY folders?! I only had around ten or so... But I waited until the window closed on its own. Doesn't that mean it's done?
EDIT: Never mind, there are 30. I don't know why I thought it was less than that. XD