Don't Fake Nihon-Jin

To put it simply, you can't do it well enough to be worth it. Sticking cultural references and occasional bits of Japanese just makes a webcomic harder to read.

A webcomic is already text & images, it doesn't need subtitles. If the use of another language is important to the story, you can always use a different font or other visual techniques that doesn't impair readability. As a general rule, anything in a webcomic that would require a footnote should be rethought. An ever worse offense is the use of random Japanese words and phrases. Sticking an 'aniki' or tossing -san and -kun all over is just. plain. annoying. Don't do it.

When using English, there is no reason to write a comic right-to-left. When a book or text reads in that direction, it makes sense; in English, it does not. When the direction of the text and panels match, it becomes easier on the eyes. Just because you're trying to imitate the style of a manga doesn't mean you should throw away common sense and duplicate everything.

Finally, the cultural issues. Japan is NOT a land of noble samurai, devious ninja and powerful feudal lords. There are not massive mafia-like networks of ancient families holding long-standing grudges. There are no arranged marriages to create political alliances or great families competing for power. If you want that, try a fantasy or historical setting.

So let's stop abusing the Japanese, repeat after me: Watashi wa baka gaijin desu!