Thanks for the trip update and glad you enjoyed Japan!
As far as the customs people treating you rudely, that's a shame. I don't think it's typical, so maybe you just caught some employee on a bad day.
Also, the time you came is right around the time of the G8 meeting, so maybe they were being more paranoid with security. If you look at the big Tokyo train stations during G8, you might see some serious looking police guys staring at everyone at they enter the ticket gates. But this is not normal in Japan, it's just an added precaution for the G8 meetings.
Hope you have chance to visit again soon!