A number of recipes from several of the Thaumcraft addons (most which I've noticed are Automagy but the same applies to some of the other addons too), as well as some Witchery recipes, do not appear to have been rebalanced to suit the enhanced difficulty of the modpack. The recipes in question aren't too significant so I do not think it is a major issue in most cases. However, the Automagy recipes for the paving stones of warding and travel probably should be either modified or removed, since they vastly cheapen the aforementioned blocks compared to their regular recipes that involve plates.
Do you have a list of recipes that need changing? If not, I'd be happy to put together a list of recipes that don't appear to have been rebalanced (I'd put it on the github of course). No guarantees that I'd be able to find every instance, but I can probably go through Witchery and the Thaumcraft addons.