I flew in and out of Narita airport. Haneda is closer to the city but the flight options for me weren’t as good.
It’s no secret that trains in Japan run on time. This is accurate enough that in one case where the station was not well sign posted and I couldn’t see the on-train screens, I was nonetheless able to get off at the correct stop because it was 3:24pm and this was the station the train stopped at at that time.
We used Suica cards for the majority of our travel. It’s a simple tap on/tap off for trains, and some combination of just tap on or just tap off, or both, for busses. The Suica worked fine across all cities we visited (Tokyo, Kyoto, Osaka, Onomichi, Imabari). They had a shortage of chips for Suica cards, so we had to get the “Welcome Suica” which we purchased at Shinjuku station. These are tourist-specific cards that last a month.
We used the shinkansen for longer journeys between cities. They were comfortable enough though for some reason I expected them to be a bit more plush. We did not book ahead, just turned up to the station and (usually) visited the counter to organise our trip. I would recommend visiting the counter, they can book the entire trip for you, including non-shinkansen connections if appropriate. Plus it’s cool to see them use the touch screens at an amusingly rapid rate (though one assistant was tapping on the side of the screen between page loads so it seemed even more hectic, it was rad!). Not booking ahead meant we often did not get a window seat, but it also meant we weren’t rushing to the station, and could plan stop-offs and stuff without having to be on the clock for the stop. We did not get a rail pass – I did the math prior to departure and for us it wasn’t going to work out, money-wise. We took 3 shinkansen trips: Tokyo>Kyoto, Osaka>Fukuyama, Okayama>Tokyo and would need at least one more long one to make it cheaper to get a rail pass. Plus the rail pass isn’t the fastest train (Nozomi) but the second fastest (Hikari).
Airport transfers were fine, though the one hitch I did have was when leaving Japan. I had carefully run my Suica down to almost nothing (pro tip: you can use them to buy stuff in konbinis), and intended to buy my last ticket to the airport with my credit card, thus leaving me with no cash. Unfortunately the ticket machine at the station I visited did not take card, despite saying it did (a local guy helped me in the end, and he was very apologetic on behalf of Japan). So I had to lug my heavy suitcase back up to street level, visit and ATM which would only let me get out cash in 10,000 yen increments, then go back to the machine and spent 1,200 yen on a ticket. So much for managing my cash well! Plus then I was so sweaty and the train was super crowded and I felt bad for both my sweaty body and my suitcase getting in everyone’s way. I did my best to apologise to Japan on behalf of every sweaty tourist…