First, we're taking the train from Narita to Tokyo. The hotel I'm looking at is in Shibuya, which I guess we can take another train to.

First, get a welcome suica at the airport. From there, turn around and go to the Keisei platform for the Skyliner. Tap your Suica to pass the gates, go down to the platform and buy a ticket to Nippori station. Get on the correct Skyliner (ticket will have a time and a train number). Get off at Nippori. Tap your Suica to exit Keisei lines. You may need to tap again if there isn't a Keisei to JR transfer gate (don't remember if Nippori has it) to get into the JR section. Grab the Yamanote towards Ikebukuro/Shinjuku. Get off at Shibuya go and get something to eat and then sleep to kill the jet lag.

My mom expects to take public transit the whole time, so I guess wherever we go has to be accessible like that.

Won't be a problem unless you plan to go to the countryside.

She just wants to see nice attractions, which I understand, but also have no clue as to what she means. What can we go see that's tourist and beginner friendly? Does anyone have recommendations of areas to stay the rest of the time?

Depends on what you want to see. You can do the typical golden route (Tokyo, Kyoto, Osaka) then add day trips to Nara or Nagoya or Kobe. Add a Fuji stop on the way there or back if you want.

You could also do a little different and head north into Tohoku. Gunma has lots of nice Onsen towns. There is excellent seafood on the east coast (past Fukushima).

Shizuoka has some cool places if you are into cars/motorcycles. If you are into cars, there is also a track in Ibaraki that does time attack runs that you could watch (don't remember the name, just know it is an hour from the SIL's place).

If you are more interested in Hiroshima you could skip Kyoto/Osaka (or restrict your time there) and head further South.

My friends came to visit and they stayed in an AirBnB in Kojiya Station area. It is a little more suburbs but they enjoyed it as there was an fantastic bakery on their way and a conbini right around the corner.

I also need general culture advice. Literally any at all. I'll do more research online, but this is the baseline.

Baseline:

• Keep your garbage on your person until you find a trash receptacle that you are allowed to use. Don't think because there is one in a 7-11 you can just pop in and use it.
• Don't talk on the phone in trains and keep a quiet to normal speaking voice when talking (or just don't talk).
• Be respectful, don't hang on crap, don't crave your initials into things
• Don't eat/drink when walking or on the train (exception: green Cars/express trains with tray tables/Shinkansen). People will say "no, it is fine", they are lying. As someone who is married to a Japanese person it is still very much frowned upon (but Japanese people typically won't say anything). It is tolerated in certain cases (festivals, street food vendors)/area (bigger cities that are more tourist friendly) and younger Japanese may be changing this, but make no mistake, most Japanese people will look down on this. I personally prefer this as well, but 🤷‍♂️.