elementalgodz11 Yes, your correct, its obviously not over-riding the minecraft mushroom stew. If this is not done by the client, you could possibly patch it. This might be done by over-riding the recipe by modifying "fields" in the Bukkit code temporarily. Maybe you could listen for the event when they craft the item, and then change it once they've crafted it.
Haven't looked into doing this myself (changing Vanilla recipes, that is), but have you tried modifying the result of a recipe via getResult()? Just a suggestion.