1. That is an unintentional error I will fix in the next patch.
2. Yes, but it requires noticing some patterns. Specifically, (ROT 13) gur flzoby ba gur ahzore gnoyrg pbhcyrq jvgu gur ahzore frdhrap jevggra ba vg. If you have audio on this is also reinforced by (ROT 13) gur abgr cebterffvba bs gur syhgr. This reading direction is consistent across the game.
3. They tell you how to get the (ROT 13) crney arpxynpr without trial and error.
4. I have no idea what item you mean by that. Every one is used at least once.