So the Passmo thing you should be fine on an iPhone. Basically when I go to add to wallet on an android (and may be my phone specifically) neither Suica or Passmo show up. When I googled it, it seemed to think I would need to change the region of my phone for them to show up but then other shit wouldn't work. My wife had no such issue on her iPhone. Just saying to check you are able to add them to your wallet pre trip.
For jetlag days I would just plan on staying in whatever city you're in and not traveling too much. There's not much you can do to avoid it and it really depends on what time your flight in is. You basically have to try to acclimatize to Japan time as soon as possible which may involve either forcing yourself to sleep all flight or not sleeping on the flight depending on what time it is. Last time we went I slept all flight and we landed in the late evening Japan time and I was messed up for way longer than I should have been.
I know people are saying Nagoya makes a good hub city and they're probably right but keep in mind without the JR Pass, it's fairly expensive to get a train to/from Nagoya/Tokyo. I forget the exact cost but I want to say somewhere in the region of $60-100 one way. So it will be pricey to make that trek to Tokyo multiple times.
Something to keep in mind with Osaka/Kyoto. They are super close to each other and Osaka hotels were small, expensive and far dirtier than the other hotels we stayed in. You can easily stay in a hotel in Kyoto that is nicer and cheaper and make the train ride to Osaka. That's what I would do if I ever did that area again
I don't have advice on Nagoya since I only did the 1 day there for Ghibli park (which is actually a decent trek outside of Nagoya) but you have a resident expert in the thread anyway. If you do do Ghibli park, you have to buy your tickets way in advance. It is entirely possible that they are already fully sold out for your trip dates already and no I'm not joking. Go check now, like immediately, if you have any interest in going there