It was awesome to hear about Chiaki's Japanese experience. I actually spent my Junior year of college at Sophia University in Tokyo (Jouchi Daigaku in Japanese). I also spent some time in Osaka, and agree with you that it's an awesome place.
As for "gaijin", my girlfriend won''t say the word, and gets pissed off when her mom does. Keep in mind though that she's often overly politically correct. Like Chiaki said, it's all about context. I only use "gaikokujin" when speaking very formally.
As for WWII memory, there is a huge mix. You have places like Yasukuni shrine which knowingly distorts the truth of what happened. I remember at the museum there, one exhibit said something close to "violence had to be used in Manchuria due to its stubborn resistance." In short, while Germany takes a stance of responsibility, Japan takes a stance of victimization.
I'm writing my thesis on Japanese minorities, so I could go on about the history. I'll speak personally though. My girlfriend was born and raised in Japan, which is where I met her. She's 1/4 Taiwanese, which is probably why her mother is so accepting of me. On the other side, her dad doesn't quite know that I exist.
As for the white people picture taking, I have to ask if they may have been Chinese? While visiting Takayama with two of my British friends, about thirty Chinese tourists wanted pictures with us...one at a time. At first it was just the girls, but then their boyfriends wanted pictures with us! My friend visited China, and said the same thing happened constantly.
Just one tiny correction: JET stands for the Japan Exchange and Teaching Program, not English. I'm not one to correct, but I've heard of people teaching Spanish through it, so I want people to know that if English is not their first language, they can still apply.
If I worked at Don Kyote and had to listen to that song, I would have jumped in front of my morning train. Speaking of which, there are more "accidents" than you'd think. On a good day, people jump only a few times in Japan. March was personally the worst month for me concerning train delays, because that's when the entrance exam results come out.
I frequented my local izakaya quite often, and saw the tie thing every now and then. It's most frequent at izakaya that offer karaoke.
I was at that comiket also! I actually went with my friend who was about 100 times the anime fan I am (I really only watch gundam). I wonder if you saw me! I was fortunate enough to take home the only four gundam comics that weren't yaoi.
Roppongi at night is actually awesome if you know where to go. I don't really view that as "red light." My outlook may be distorted though because of the three years I lived in New Orleans. Although when walking home, there was this creepy Nigerian guy who always asked me if I wanted a massage. That was weird.
My friend who I lived with in Japan makes a Japanese video blog about our time there. We lived in an actual red light district, and he takes us on a walk around town. http://www.youtube.com/watch?v=Wftp4WIQ1Mg&feature=fvst
This is one of his few videos on his channel that I'm not in, so I'm being as unbiased as possible. Enjoy!