Aeroblyctos says there's a way to unstack, it's right clicking on the item you want to unstack then left clicking on a different slot in the inventory. I haven't tried it yet myself. Also, there's another way to make the recipe work. When you get the magic balls, you put each one in a different box. You have 6 boxes per hero, why not put a magic ball in each one? It's useful for when you need 1 magic ball for a recipe or 5 magic balls for another recipe. You can stack them when you need them.
About the 'Choose mission', you can use the 'give up' function. It enables you to repeat the whole campaign with the gold, honor and lives you currently have, so you'll have an advantage the next time you play. You can use it to go through chapter 2 again to get the thief set.