just rushed through stages 2-3-5 but didn't encounter any of the bugs you mentioned so it sadly seems to be specific to you or something you have done outside of what was mentionned.
but since you are able to modify the savefile, you have the option to bypass the crystal door requirement by altering the WEQuest variable to 6, through i would understand if you do not wish to pursue your playthrough after this incident.
PS: if you could provide a screenshot of the room containing both the door and the space past the right wall, i may have better luck at identifying the issue.