Hi DARTHJAVAGA, welcome to the forums,
I am sorry to hear that this issue is affecting your save, thank you for reporting it and for using the bug report format to do so 
There is an issue that the team is aware of affecting the crafting menu at the moment that prevents the story items from unlocking, however some players have found a workaround for the issue - if you use the quickcrafting menu you should be able to craft the items. In some cases you may have better success if you are at the boss area when you try this.
Unfortunately due to the locked items in the crafting menu, this may affect achievements such as “Gotta Craft Them All”. There is also an issue with the achievement “Call Me Ahab” unlocking too that the team were investigating. If achievements are something you wish to unlock, I would recommend returning to the starting island to craft each of the trophies there if at all possible.
I have known issue reports on both of these here if you would like to read more: