Henbaka-san,
You are not ignorant - not my intention at all! I was surprised myself when I was told I had to leave my passport with the embassy for them to process. I have never had to do that before.
As far as I know this is still the practice in Tokyo. So yes, you need to take a passport photo as normal, but you will still have to wait for the embassy to process your request... unless things have changed. If you find out they have then please let us all know as I think many members would find this useful.
Good luck Henbaka-san
