I'm checking the teleport to the headmistress's office door and I see that it works. Is it possible that, because of the bug where you were in 4F and went to 3F when entering the music room, you got the wrong floor and tried to enter the headmistress's office from 3F and not 4F? If not, I'll check again.
Regarding going to the bathroom and getting stuck, I'll check it as soon as I can, I'm sorry you found that bug.
Let's see, the secret ending works like this: when you unlock the first five, you can start a new game, go to Mayuri and Asuka's room, pick up the letter, go to Yuri's room, see the sex scene, at the end of the sex scene you have to make a decision: "Yes..." or "No!" You select "No!" and the game teleports you to a map full of chaos. There you should only have one possible path that leads you through several maps to the gym. Any of that not working?