If it makes you feel any better, government offices in the States are notoriously hellish experiences as well.. But you can usually sue someone.. or shoot them.
Here, you're just another FUCKED GAIJIN! Welcome!

british drivers licence holders don`t need to take a written or practical test
Get an international license. Why do you need a worthless Japanese license?
Or, don't get a license at all. I drove for ten years without one.. You actually drive MUCH better!

Or, make 4 copies of EVERY possible paper size. Then make them choose which one they need. It's always nice to jiggle those Japanese ben WA balls.
GJ