There is only 1 puzzle here, and having 2 empty inventory slots at this point is correct.
The clue you are wondering about is for finding an item you already got (the crney arpxynpr).
Viewing post in ng gur nepuvcryntb nz v zvffvat nalguvat
I think you've misinterpreted some things.
1. I have no idea what you mean about "gur zf va svyr q ner onpxjneqf". No one else has reported issues there and it looks correct to me.
2. Lbh arire unq na vgrz va gur pragre bs lbhe vairagbel va gur svefg eha. Hagvy lbh unir fbyirq gur svany chmmyr lbh fubhyq unir 2 rzcgl fybgf - gbc-yrsg naq pragre.
3. Consider Occam's razor.