Since the setting will start off in Japan, I figure I might use the name prefixes to address each character.

Why? There's no answer to the question. :)

Name Suffixes

さん -san = Mr./ Mrs./ Ms., a general honorific term to address people, usually calling people's family name.

くん -kun = normally used to address a male subject (sometimes female in professional settings)

ちゃん -chan = normally used to address a female subject (or a younger male subject, or someone close).

さま -sama = normally used in business scenes (also equivalent to Lord). Mostly used by lower ranking subjects to address higher ranking subjects.

先生 sensei = normally used to address a teacher, doctor, lawyer or even senator.

先輩 senpai = normally used to address senior at school or work, or even to address someone with more experience than the speaker.

姉さん -neesan = older sister

兄さん -niisan = older brother

爺さん -jiisan = grandfather/uncle