So ExactChoice works perfectly with shaped recipes but I've run into one small issue. ExactChoice items wont automatically insert into the crafting table when you click the item in your recipe book when you have items needed in your inventory. If you have all the items it also doesn't change from red to white in your recipe book. 

Gif: https://gyazo.com/5c2a185de47b49a95db57517cb6fb1ed

In that gif, emerald armor is normal, redstone sword is exact. Redstone ruby is a reskinned clock with a custom model id and displayname.

if (!exact) recipe.setIngredient(cKey, RecipeMaterials.valueOf(rID).getMaterial());
else recipe.setIngredient(cKey, new RecipeChoice.ExactChoice(RecipeItemStacks.valueOf(rID).getItem()));