I could not agree more about the pachinko parlors, I had to leave quickly.
But I had the exact opposite experience with the train system, and I'm definitely not used to using one. But it was probably made simpler by the fact that we were told to get Pasmo cards, which could then be filled up using automats, and it was really simple to just walk in and out wherever and not having to use tickets. But the maps and which direction stuff went in and things like that weren't as complicated as I would have assumed considering the size of the city, I was only surprised once when suddenly the train didn't go any further than some place midway in the route, but I just followed the commuting people into a new train and it worked out okay (it could definitely have turned out "not okay", but the train pretty clearly stated it was heading to where I was going, the only slightly worrying thing was that it was late at night and the trains stop running pretty early, so if I was wrong, I'd have been fucked).
And I felt really lost with the amount of Japanese, even though a lot of things, like names of places and stations were in English. And it was way more confusing than other countries where I didn't speak the language either, simply because I couldn't really recognize words or letters either, so it was just super confusing all the time, but luckily I hung out with someone who's sort of in love with a lot of things Japanese, and she knew some of the signs and words. And some places do use English (or, well, the Latin alphabet), it was just really weird to not even be able to attempt reading or understanding words around me.
But then again, I don't think Japan and I mix very well. Definitely interesting to visit, though, and it sounds like you've had a great time!