When using the recipe maker on a table in which enchanted books are present you get "minecraft:enchanted_book.withTag({StoredEnchantments:[{lvl:5s,id:16s}]})" as syntax but CraftTweaker doesn't work with this syntax and instead you need "minecraft:enchanted_book.withTag({StoredEnchantments:[{lvl: 5 as short,id: 16 as short}]})". So you would need to fix this because it's quiete tedious to change all of these manually especially if you are using a recipe with lots of different enchanted books. (Bold italics are there to show which part is wrong and how to change)