Phew, okay... finally I can head to bed after I post this.
PLEASE READ THE MAIN POST AGAIN AS IT HAS BEEN UPDATED DRASTICALLY!
With the release of patch 1.0.1, I decided to label problems as fixed, unfixed (remains), or still needs testing. Sometimes you will just see "(1.0.1)" which means I only noticed it after the release of the patch, so I wasn't sure if it was a problem in vanilla or not. I have also split the fixed problems from everything else and now have two separate posts. If you have a problem which has been fixed, just say so and I'll update it accordingly - likewise if a problem has surfaced because of the new patch.
I just retrieved the three orb pieces from the Transept and I'm tired as hell, so I haven't tested anything past that. I may have also messed some things up in the main posts, but it'll have to wait because I'm just too tired.
Thanks to everyone, again, who've contributed to this list and let's continue to help Frictional perfect their game.