This is a tough one for me. I first came over in 2001 so my memory is a little foggy about the little things that I am sure I noticed back then, but are normal to me now.
One thing I clearly remember was the scents. Everything smelled different, both good and bad. Incense, yakimo, air fresheners, the plants, etc. all foreign.
Some obvious things, toilets(holes in the floor), delicious food everywhere, an amazing transportation system that ran on time(fuck you MUNI), the vastness of the Tokyo. The latter still blows me away to this day. I have wandered the streets here for years and I only know a very small fraction of the city. Even then shops come and go.
A good cup of coffee is still hard to come by though. We have some great brewers in Tokyo now, but like you said, it's taken years. I was spoiled with Dietrichs & Kean.
Dietrich’s & Kean? That’s a brand I don’t know.
That’s interesting that you remember the scents. That doesn’t stand out to me. I’ve heard a lot of people talk about all the new sounds over here, which there are many, but if they hadn’t have been pointed out to me, I don’t know if I would have noticed them.