How would I make an object that when it is crafted it is given a different NBT value depending on the ingredient.

here's an idea I've had, make the recipes look like this

       

        addShapelessRecipe(CustomSword, 0xf600ff, clay, obsidian);

        addShapelessRecipe(CustomSword, 0x00f6ff, CustomSword, obsidian);

 

and add this function here

 

            public static int addShapelessRecipe(ItemStack output, int ii, Object... params)

    {

        CraftingManager.getInstance().addShapelessRecipe(output, params);

                return ii;

    }

 

My only problem is I don't know how to get int ii from my mod_ file to NBT data in my item file.

You need to make your own recipe class that implements IRecipe. Then add it with GameRegistry.addRecipe(yourIRecipe);. look at some of the classes in net.minecraft.item.crafting for examples of this.