OK, I think I managed to fix most of the bugs you listed. Thanks a lot for listing them, I guess it took a lot of thinking and trying random stuff to find all of them. I will upload the updated version of the game after I finish my replay (I'm playing rather slowly because of work and the new Pokemon game)
I always try to have all locations in mind that I can visit at any given moment (and if there's a reason for another visit), so with and in a game as huge as yours, some mistakes are bound to happen, but considering your game's scope, you didn't let much or anything serious slip through. Players like me, who scale the Tower of Ragnarok in your game a second time (just because it wasn't possible before to explore the boss room manually), tend to maneuver themselves into tricky situations (on purpose). :D