[Vexx]

I'm not going to say you're totally off-base but the way you're putting it is somewhat extreme. I could describe cultural etiquette of the US in such a way that it would sound like we were living in a nuthouse of a place.

But just to address the points...

Spoiler for for space saving:

-When talking to someone, there's always someone "superior" and someone "inferior".
Knowing the hierarchy of seniority or position is important and alters the form of language you use. Much like the way you speak amongst friends is different (or had better be different) than the way you speak to your boss.

-Bow: The inferior one needs to bow at 30 degrees and longer, the superior one can bow more quickly at 15 degrees, or just nod. The superior gets the cool endname suffix, and the inferior gets an ordinary one or -chan at the end as an insult(you're a child).
There is a bowing etiquette (much like military etiquette or social etiquette).
Everyone has a post-title honorific (usually -san). -chan is not an insult. Its a term of affection for a young child or a girl with you are on close terms. Calling someone without a suffix means you're either very close (married, etc) or its an insult. You *always* refer to yourself without suffix. Using a suffix on yourself would be presuming too much.

-Japanese never say what they're really thinking because they want to avoid conflict, and remain polite at all times. If asked "Would you like tea or coffee?" they answer "Either is fine" because otherwise it is impolite, and can only say which they really want if then asked "Which one do you prefer?" "Tea"
Japanese often say what they're really thinking. They just are extremely polite about it or phrase it unconfrontationally.

-They look for hidden meanings in everything that's done and said, cause they never say their true thoughts.
They don't have to "look for it" .... its obvious if one is paying attention. I could easily say one should look for hidden meanings in any culture.

-Men are expected to be aggressive and rough, women are expected to be submissive and gentle.
An extreme way of saying it, but not much different than the US until the 1960s (or even today based on some of the crap I hear in public). The japanese don't rank well by country in terms of women's opportunities and equality - but all the archetypes you see in anime are represented in some way by real people: soft-spoken males, noisy females, tsundere, nadesico-types, brash grunting males.
The "aggressive and rough" male is sometimes simply a difference of pronoun usage and using the particle "yo" more often.

-When they're polite, they don't actually mean it, it's just an automatic reaction.
Andddddd, this is a bad thing? I wish politeness were an automatic reaction in my culture.

-Sometimes they refuse gifts because they think there are strings attached.
They don't refuse gifts... but gifts and favors imply obligation. They like the favors to balance out.
When you ask for directions at the train station, japanese will sometimes go way out of their way to help you since you have obligated them by asking for help. So be modest in asking for that reason.