I wish to have an item that could be put in a crafting table with a "modifier" item. Based on this item, the crafting result would be the first item, but with a modified nbt. But I have no idea how this would be done.

I would use an Item Crafted event after you have registered the standard crafting recipe:

 

 

 

...


public void ItemCrafted(ItemCraftedEvent event) {

	if (event.crafting.getItem() instanceof XXX) {
                        ItemStack craftedItem = event.crafting;

		List<ItemStack> potions = new ArrayList<ItemStack>();                         //MODIFIER ITEMS USED
		ItemStack usedFood = new ItemStack(Items.bread);

		for (int slot = 0; slot < event.craftMatrix.getSizeInventory(); slot++) {
			if (event.craftMatrix.getStackInSlot(slot) != null) {
				if ((event.craftMatrix.getStackInSlot(slot).getItem()) instanceof ItemPotion) {
					potions.add(event.craftMatrix.getStackInSlot(slot));
					event.craftMatrix.setInventorySlotContents(slot, new ItemStack(Items.glass_bottle));
				} else if (event.craftMatrix.getStackInSlot(slot).isItemEqual(craftedItem)) {
					usedFood = event.craftMatrix.getStackInSlot(slot);
				}
			}
		}


                        .........

                        craftedItem.setTagCompound(nbt);


}}
...

 

 

 

This is what i use in my mod. But be aware that i wrote it 5 months ago in not more than 10 minutes, so its definitely not resource saving and most likely i ignored the java coding conventions. (But hey, it works)