Acknowledge but can’t include in Koseki

Hope all is well!
Would appreciate your time on reading through my comaplicated case. Im 34 and I have a japanese father who just recently contacted me. He abandoned me since birth. I was registered under his surname upon birth but since he has been a no call, no show my mother has registered me under my stepfather's surname when i was 6 yrs old. She was not properly guided back then by the local civil registrars. So i have been using my stepfather's surname my entire life until last Y2K bug and govt use computers already, NSO only recognizes my japanese registration and has erased my filipino surname registration. Problem is my BC surname doesnt match my passport surname. We filed a court case for correction but it was denied. Also my father is willing to acknowldge me but he cant put me in koseki touhun as he cant let his japanese wife know i exist.. i need advise. Do i stand any chance of getting citizenship?

Without being officially registered in a koseki tohon, I think it is not likely. Go see the Japanese embassy in your country.

Thank you for the prompt response. This has been bothering me especially that Im about to apply a 90 day visa to meet my father as he is sick. What if he would be willing to include me on his family registry will the surname issue affects the process? and im no longer below 21 yrs old.