Despite the fact that the Immigration Office is way out on a peninsula of reclaimed land in the bay, conveniently located a bus-ride from Shinagawa Station past the fancy new trash and recycling center, getting my new Foreign Residence Card wasn't nearly as painful as I thought it would be.
Got off the bus, asked at the Info desk, was given one piece of paper and directed to the photo booth.
Took my photos, went to the counter to borrow the available scissors (to cut off the bottom row of photos), square puncher (to cut out a single photo in just the right size), and glue (to affix said photo to said form), then with form, old card, and passport in hand, I proceeded up to the second floor.
...And was greeted with a scene out of a CNN special on refugee camps of war-torn central Africa or something.
Huge lines of people, babies crying, people screaming, talking on cell phones, sitting around randomly and zoned out; complete human chaos.
Luckily that was the "applying for a visa" zone, and I had to go around the corner to the "get my new residence card" zone, which was much more subdued.
Confirmed I was in the right place, grabbed my number, sat down and pulled out my laptop to be productive. Number was called in about 20 minutes, so I handed over my stuff and was given my number back.
Ate two cookies, pulled out the laptop again, and about 40 minutes later had my new card in hand!
I was so excited I decided to press my luck, and went to apply for registration to use the automatic immigration gates at the airport.
Another window, another single piece of paper form, another number, another 20 minute wait.
Handed over my stuff, scanned my finger prints, facial photo taken, and 10 minutes later I was registered. Only issue is the registration only lasts until my passport expires, which is in less than a year, but still, small wins!
Three cheers for efficient Japanese bureaucracy.