/jp/ - Otaku Culture

Can someone explain the Japanese "student/school culture" and other knickknacks to me? What is fact and what is fiction? I've only watched a lot of anime, but it seems

It is a very big deal if you are late to school (but main characters in anime are always running late with a piece of buttered toast in their mouth),
seniors treat the freshmen like underlings and have a very strong sense of pride,
students are divided by homeroom classes with a number and letter (ex: 3-F) and students introduce themselves by this,
cool kids eat lunch on the rooftop,
common clubs include: track, swim, and kendo (otakus are looked down upon)
girls wear bloomers,
there are guys who secretly take photos of popular girls and sell them,
girls sell their underwear,
students wear "long" versions of their uniform jackets and skirts as a sign of rebellion,
etc.

Are there any other big ones?