Loud chatter or behavior is usually frowned upon because it invades others' space. Avoid talking on the phone (put it on silent) and send messages instead. Eating and drinking should only be done on long-distance trains.
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Shorts, jeans, and camisoles are perfectly fine to wear as long as you don't plan on attending religious sites. While denim isn't a popular fashion choice for those beyond their teen years, black jeans are more acceptable due to their versatile nature.
I wouldn't say it's considered rude, but it's just not really normal, especially in bigger cities, and definitely not in Tokyo. It is possible that you could look a bit crazy or suspicious if you make a point of meeting people's eyes and smiling. It could also lead to misunderstanding.
In fact, in Japanese culture, people are taught not to maintain eye contact with others because too much eye contact is often considered disrespectful.
Try to be mindful of the type of shoes you're wearing, as certain shoes, such as sandals, might not be allowed in some indoor spaces. If you're given slippers at the entrance to a building remember to wear them inside only! We know they're comfy but these aren't meant for sightseeing or as a souvenir!
People who live in Okinawa, Japan have a wise strategy when it comes to maintaining a healthy weight. They call it “hara hachi bu”, which means to stop eating when you are 80% full. Studies show that cutting back on calories can lead to better heart health, longevity, and weight loss.
Tipping in Japan is not expected, and attempts to leave a tip will almost certainly be turned down (a potentially awkward moment). In Japan, it's thought that by dining out or drinking at a bar, you are already paying the establishment for good service.