Permanent Residency question

My father was Japanese when I was born, so I am registered in koseki (I have a copy of it). My mother is Taiwanese.
I was born in America and have American Citizenship. Till three years ago, we've lived in the states and my parents have both become naturalized US citizens.
My father has renounced his Japanese citizenship.

So both my parents have re-entry permits in Japan. Technically my sister and I are Japanese citizens due to koseki and the fact that we are both under 21 years old. HOWEVER we both have re-entry permits because we didn't apply for a Japanese passport.

I am 17 now and will be going back to the states for college (2010), but I will be coming to Japan during school breaks and summer. What happens to my re-entry permit, can I apply for permanent residency even though I am not living in Japan? Both my parents qualify for permanent residency in two years. Is it beneficial to apply for a Japanese passport now? Will it conflict with my re-entry permit?

I'm not sure but I don't think you could apply for PR as a minor. If I were you I would just get a Japanese passport and not worry about visas and re-entry permits.

I'm curious: what does your koseki look like now that your dad is no longer Japanese? Who's listed as the head of household at the top?