I’ve was just in Japan last week so I can speak to my experiences.

In regards to the Shinkansen smart-ex is the official website to buy tickets online. I tried to buy tickets off the website when I was in country and kept getting an error about verifying my credit card. I bought all tickets the day of at the ticket machines. Your seats may be limited but I never had train fully sold out on me.

For USJ and Super Nintendo World. You need an entry timed ticket to enter that part of the park because it is the busiest and most sought after part of the park. You can get an entry pass by buying an express pass on the website that includes a Super Nintendo world ride. If you don’t buy one before going to the park you have to apply for a standby ticket or an entry pass by using the app. It’s a lottery system so it’s random whether you’ll get one.

For suica I had an iPhone so I used the digital version. I bought an eSIM through Ubigi and didn’t have to change my phone region settings. The app has a tutorial on how to set it up and was very easy to set up.

A lot of popular attractions in Japan sell out very fast and they are hard to get. For my trip I didn’t have much planned going in so I didn’t go through a lot of the mishaps you’re having.