Thanks for the post! I will be posting an update fixing some bugs that have been reported by others, maybe sometime tonight or tomorrow.
You should be able to finish the Masked Man section the way the game is now if you have all the items, but I will take another look into it, just in case. Some of the side quests have very convoluted ways of beating them, or have no "ending" at all.
Also, from what it sounds like, you still have a bit to discover! Thank you for playing!