Hey, congratulations on beating the main story of the game, and thanks for playing! :)
I'll answer your points one by one.
Regarding the missing orb -> I looked into this in case I made a mistake, but from what I could find there doesn't seem to be anything wrong. I don't really want to spoil too much, but did you find the "Translation Script (A)" and interact with the stone monument in the Star Desert?
Now, the keys -> They can be used in the post-game dungeon you're missing right now because of the orb. Edit: There could be a bug regarding the use of the keys. I'll look into it and upload a fixed version later tonight.
The missing eye -> That's a mess-up on my part. I overlooked this event since I did plan on making something out of it, but eventually turned against that idea. Instead, the dragon statue riddle in the Desert Ruins took its place. I apologize for the confusion here.
The dead ends -> That's correct, there are no areas beyond that point. I simply designed those "exits" to imply that something lies beyond. I found it better because of world-building.
The side quest -> That should pretty much cover the implemented quest with a few exceptions. I'll get back to this one after I'm home.
As for all the other crafting-related points -> I'll look further into it once I'm back home from work later tonight. :)