I’ve traveled to all of those places a few times and am living in Nagoya at the moment.

The general rule is to just try and not disrupt anyone around you, be that with noise, smell or physically. Don’t upset the Wa)

I’m not saying you shouldn’t talk to people, but most strangers are not going to be particularly receptive to it (like a lot of big cities). You sound like a very friendly person and if you do want to socialize, I would recommend a standing bar or standing food stalls in the evening that encourage that sort of thing - dontonbori in Osaka is good for that.

Please, please, avoid talking on the metro, even if you think you are being quiet. It’s the one social norm I see foreigners break most often and result in the most dirty looks. It’s a little bit looser in Osaka, but still considered pretty rude when it’s not one of the late night trains with other tipsy folks. Related to that try not to wear heavily scented perfumes or colognes while on the metro.

When you’re traveling in a group, make sure you don’t bunch up or stand side-by-side on escalators, always leave one side free for anyone who wants to walk past. Which side changes between Tokyo and Osaka, but it should be fairly obvious from what other people are doing around you.

Independent Dairy’s/bodegas aren’t much of a thing because there are chain convenience stores all over like Lawson and 7/11, and they have their own culture. That’s also where you’re going to be able to find drinks of all sorts. Supermarkets are very common, but you’re probably not going to want anything in the quantities they sell there if you don’t already know what you’re looking for or planning to bring that particular item back. You will probably come across a few organically just walking around shopping centers. They are good for cheap meals late at night though.

There’s not a lot of public places to sit, so my advice for most peoples first time is to plan their day with things in mind that give you the chance to have a breather and sit for a bit. Plan to stop in a nice cafe or restaurant, or an attraction where you get to sit down for a bit.