@Daiima - some of the things that I did that helped:
Trying to be very considerate of locals when catching / riding trains - queue properly, use the overhead luggage rack or your lap rather than have a back-pack on your back or on the floor (or use the wheelchair areas at the ends of some carriages if carrying extra luggage on regular suburban trains).
A few times I've offered my seat to elderly people or a younger group of people who could otherwise not sit together - you only need say "Dozo" (Please) when offering your seat.
"Sumimasen" is a term both for when you might need to squeeze past someone or when calling for attention at a shop counter or in a restaurant.
If you are travelling on your own, you won't be like a noisy group of tourists.
If you print out Google Maps print-outs of specific places that you want to visit, you can show them to locals if you need to get better directions.
A few times when locals have seen that I am on my own, they have offered to take my picture, or asked in English if I needed help or where I was from, so it's good to know the Japanese phrases to say where you are from and what nationality you are.
It is really fun to be the only westerner at a concert. Bring along pictures of your favourite artists with their names in Japanese if you like - you might see someone else with t-shirts, towels or bags for that artist. Usually they keep to themselves, but some are happy to say konnichiwa when you are queuing.
Japanese feel the same way sometimes when visiting Paris:
https://en.wikipedia.org/wiki/Paris_syndrome
. I have a friend who lives in outer Tokyo so she's being helpful, at least, plus I know another guy who teaches English over there and someone who studied there for half a year, so hopefully I'll have plenty of info sources. I don't even want to know how much I could spend, though, that's worrying me a little more than actually finding my way around 
.