Here's a thought, you know why the author set his anime about an italian mafia in Japan? Because he's Japanese, Japan is his country, it's the culture and locations that he knows and can thus integrate into a setting more or less accurately because he lives there. Not just because he thought it'd be cool to set it in Japan because other works set it in Japan. 

You're actively shooting yourself in the foot here and letting go of a workable idea because you absolutely want to set it in Japan when it doesn't make sense for it to happen there and when you can't really work with Japan as a setting, by your own admission, instead of making up your own country where all of these issues would be moot, man.