Usually the person leaving says "Otsukaresama desu" because the people in the office are still working and the people staying say "Otsukaresama deshita" because the person leaving ...

There's no Chipotle, but something similar is Frijoles. Not as good in my opinion but pretty close!

When the train is delayed, the print the date and the length of time the train was delayed so you can take it to work as proof as to why you are late.

They sell Claritin and Japanese equivalents at drugstores, no prescription necessary. But if it's really bad, you can get a prescription at a local clinic.

I don't but a lot of people carry folding umbrellas. I always get an convenience store umbrella if it's raining that much.

Depends on the job! Some jobs require you to have your natural hair color and others don't care so much. Blonde on an Asian stands out in say, a hospital or government office. But maybe not so muc...

This site was helpful for me. https://www.taxesforexpats.com/japan/us-tax-preparation-in-japan.html

I have a tattoo and it doesn't really affect me on a daily basis. I can't go to hot springs or the public pool, but they're not my thing so I don't feel like I'm losing out on much...

Nope!