I'm trying to make an item that when you right click it will cast a spell based on the nbtdata now i've gotten that to work, but as it is now the player has access to all the spells the book has. I don't like that i would like to make where the player starts out with one spell and they have to craft it  together with a piece of paper to gain access to the next spell.

 

so what i'm really asking is how to tell when an item is crafted with another item and update the nbtdata accordingly.

 

(and i know i could just make a munch of separate books with each one having one more spell then the last, but i really didn't want to do that)

Look at how the fireworks are crafted with various items to create different effects (RecipeFireworks), and how leather armor is crafted with dyes to make various colors(RecipesArmorDyes). These both modify NBT tags after crafting.