pass1

There seems to be some empty desk spots. Try to imagine what the desks would look like if they were shifted to the left.

pass1 - solution

The code is 91074 but the "0" is a random number between 0 and 9.

pass2

Maybe the triangle can help.

pass2 - solution

The code is 50660 but the last "0" is a random number between 0 and 9.

pass3

AB:

Each AB contains a Chinese numeral.

C:

Multiply by the left numbers, then do something to get the right number.

pass3 - solution

Translator here, if you're having a hard time with pass3, don't worry. Other people have struggled with this too because this is, by far, the hardest puzzle in the game. The Textbook is supposed to relate to the map of Japan (hence "KITAMOTO"), with "BA" relating to numbers that correspond to the names of those geographical locations. Alongside that, the lunchbox and the teacher's desk contain some form of numerical graphs that explain how to get C. If you don't want to have the answer revealed to you, please stop reading this hint. However, if you feel that you've had enough and just want to finish the game, uncover the following text.

pass3: 539.

All items have been used.