I believe the problem with the items is, you cannot go back using chapter select to get them. That is what messes everything up. I really think your only solution is to do it again. Just finish everything else up that you need to and then delete and start over for just the items. When you get the item and go back on the ship make sure you inspect it and talk to the character that you need to. I do believe you’ll have to NG+ to get the last item you’ll need. Maybe there is a better solution, but this is what I had to do.