It’s pretty different living in Japan as a foreigner. For one thing, the spaces that you live, especially in Tokyo, are an every-day reality rather than an exotic experience, which might be hard to adjust to for some people.
Being unable to read Japanese will get to you, especially for administrative things to settle in. I can get around it because I can get by with Japanese and have always lived with fluent Japanese people.
People in the service industry are still polite. Basically it’s their job. You’ll just have things work around you as a foreigner, which can be insulating and/or exclusive.
The places that tourists are willing to travel for all in one go are probably spaced out over years for Japanese, if ever, as they’re costly to get to and from a domestic perspective, might not be as exotic as going to SE Asia for example.
The JR pass doesn’t work for people who live in the country (nationals or foreigners).
Nonetheless, I love Japan as a traveller and as someone living here and I’m glad you had a great time. Many of the things you enjoyed are also part of people’s regular routines — such as visiting the food halls every week or two! :-)