In reply to DaewooOfDeath :
Well, the context certainly explains a lot of your fundamental outlook. You grew up in nearly universal chaos and conflict, so of course you have developed coping strategies and a power-forward outlook centered around establishing a safe niche for yourself.
To your very very great credit, you seem to have avoided becoming an aggressor and have focused on the defensive side.
Now that you have (more or less) escaped the chaotic environment of your family life and original location, you are entering the decompression phase. That decompression is complicated somewhat by the differing cultural biases of your new home, so you are having to relearn not one but two new societal systems: 1) living in a community that is not based on fear, theft, and destruction, and 2) the general conformist expectations and rigid hierarchy of status in East Asian culture.
So let me say flat out that I think you're doing great so far.
Your genetics are probably going to keep you a gringo to some extent, no matter how hard you try, but that's not changeable, so just keep working with it. I don't think you need to try to become "more Japanese than Japan", but it will serve you well to continue developing your understanding of and sensitivity to Japanese culture. Just doing your best to avoid making mistakes in etiquette should be enough and should be appreciated by those you interact with.
Continuing to improve your Japanese language skills should go a long way. For instance, in France, many people speak usable English. However, if you approach them only in English, they're likely to just blow you off and pretend they don't. But if you make any effort at all, even just learning the French for "Hello, sir, pardon me, my French sucks, but can you help me?" they are often willing to help. I can only imagine that your efforts to learn Japanese are appreciated the same way.
The other half of your task is to learn that most of the social environment is not as chaotic as what you grew up in. Most people are ambivalent to most other people by default, and a little courtesy goes a long way. Most people are not going to anticipate a potential for a deeply important, high stakes interaction most of the time.
For instance, another reading of your peanut allergy example could go like this:
Someone tells you they have a peanut allergy just as a topic of discussion, not as an admission of weakness. They almost certainly wouldn't consider it a demonstration of their trust in you. It would just be a statement of fact. And in return, you might have the allergen menu sent over as a simple act of empathy and a gesture of courtesy, rather than to prove the point that you are covering for their vulnerability.
Let me restate that I think your self-awareness is great and I have confidence that you will learn to adapt to a more stable, lower-pressure environment. Just keep an eye on your own responses. When you find yourself overthinking a situation in terms of conflict and strategy, see if you can reframe the interaction in terms of empathy and courtesy between friends (even if they're not actual friends). That won't always be right either; there is still a general need for situational awareness and self -protection. But I think you've had to be at Defcon 2 or 3 for so long, you need to consciously let yourself dial it back to 4 and eventually 5.
Good luck and please keep us posted on your progress. We're always here to listen and even if there is the occasional shiny happy person, no one here can actually hurt you even if they wanted to. The worst they can do is be a dick and dicks are easily ignored.