I don't know if it qualifies as long distance, but I have traveled across Japan a couple of times on train, from Sapporo to Fukuoka. Not in one day, I stopped for a few days in between, but I have done Sapporo to Nara and Kyoto to Sapporo in a day.

I loved all of them, worst train journey I had was Tokyo to Osaka... landed in Japan, slept overnight at an Airbnb and got up to get on the train to Osaka, but we missed our first train... was not a problem catching the next one, but we decided to eat lunch first. Got on the next train and got about 1/3 of the way to Osaka when the train had to stop due to a typhoon. We were stuck in the train for hours, by the time they let us off (we were stopped at a station, but not at the platform) it was too late to book any lodgeing anywhere near the station, and all the food was sold out everywhere nearby. We ate snacks we brought with us and slept on the train station floor! It was an adventure for sure. But things like that can happen when flying too and are quite rare on Japanese trains.

Don't have any experience with cross country train travel anywhere else, but I love doing it in Japan!