On day 4 of this walkthrough...
http://www.funny-games.biz/robozou_walkthrough.html
it says, There must be three choices!

But when I get to this point there are only 2 choices. I've followed the walkthrough exactly (even as far as not picking up any items). By day 4 I have 500 experience but when sleep comes there are only two choices.

On day 3 the walkthrough also says enter/exit all the 4 tunes. What does it mean by tunes?

I think it means rooms not tunes,and if you dont get three options use the vacuum more,when you do get 3 choices,if i remember right the teacher comes to get you out of bed then you get control of her.