I took the Shinkansen to Okayama and crossed the Seto Ohashi Bridge by car. I live in the countryside (Kanto) and when I went to Kansai for sightseeing, it was difficult to know which train to take to get to my destination. But it was fun
Same, I watch a lot of the Solo Travel Japan videos on YouTube and find some of his trips inspiring. I've actually started learning some Japanese during my free time so that when my wife and I do go I can at the very least try to not act like a disrespectful foreigner lol. Sadly, my tattoos have pretty much ruled out my wife and I from visiting any ryokan, as pretty as some of them look.
Only been to Japan twice that I can remember, but always used rail to go to/from Tokyo to where my mother's home town is on the southern end of the country. Also got to ride behind a DD51 last time I was there when we were visiting a town somewhere in the mountains.
Be sure to bring cash. Even in Japan, some stores only accept cash. Please be careful when changing trains. The closer you get to the city center, the more lines there will be. For the first time on this trip, I slept on the "Special Rapid Service" train bound for Kyoto, and when I woke up, I was in Kyoto. So please be careful when transferring.
Well that's one thing that would not be a problem for me at least. Before I got my disabled bus pass, London transport always frustrated me any time I visited because I like to use cash for everything.
For any train, but especially the Shinkansen since you'll likely be on it for a while, if you are going into the free-for-all non-reserved seating cars, I'd recommend lining up around 15 mins prior. If you are catching the train from the originating stations like Tokyo, Osaka, Hakata, or the main terminals along the line that have a yard, chances are very likely they'll pull the train into the platform and leave the doors open for the 10-15 minutes leading up to departure. Furthermore, even at intermediate stations where you might not necessarily get a 'fresh' train, people are always disembarking in sizeable groups. Other passengers, guaranteed, will begin queuing up 15 or even more minutes prior to departure time, so the closer you are to the front of the line, the more likely you are to get a seat favorable to you.