Just got back from Japan Sunday. Here's some advice.
Disneyland and Disneysea do mid-week. We did a Tuesday a week apart. I made the mistake of staying way too far away on the first visit, and got to Disneysea too late to get Fantasy Springs entry. Oh well. Disneyland the week after rained all day, so lines were fantastic! The park was empty after around 7/8pm except for Main Street.
Universal - that park is a mess. The Express Pass can only do select rides; you opt for 'packages'. We found single rider OK. Still struggled to get on everything with the 1.5 day pass. Unfortunately we missed the fact it needed to be consequent visits, so had to spring for a second day pass.
We got Nintendo entry at around 11am still. This was on a weekend too, mind you. But if you can get up early and/or stay on site, try to get it as early as possible. You need to scan in to get the app entry, not just be on site.
Disney/Universal park hours reportedly open an hour earlier than posted times. We didn't get there early enough. Staying til close helps also, as people tend to leave after the main show/parade but Universal in Halloween is still a mess.
The locals LOVE shows/parades/anything they can take photos of. Use this to your advantage and go hit the rides first/last up.
Staying at a resort also allows you to get pass outs (or can you make other excuses? Who knows).
Nagashima Spa Land ops are a joke. Go on a quiet day and still will struggle to fit everything in. Steel Dragon is amazing in the last row. We paid the $15 (or was it $10?) to get express pass one time.
In Tokyo, it felt like everything was 40-50 minutes travel from one another. No matter how close it appears on a map. We changed our hotels halfway through the trip to stay on site, ended up making life A LOT easier.
I don't really have any specific advise but feel to PM if you have any questions.
I found Japan really easy going and quite tourist friendly, SO LONG as you have something like Google Maps to assist with transport. Make sure you go get a Pasmo or Suca card (QC) ASAP when you land - otherwise every train line basically has its own company and ticketing systems. The Go Card-like cards allow you to top up and you can use these throughout Tokyo, Osaka, Nara (and I assume elsewhere). Google where to purchase.
You just buy your Shinkansen (bullet train) as needed. Don't fear unreserved seating, we did this as we decided to do an open jaw booking (Osaka to Nagoya then on to Tokyo the next day).
Hmm what else. Make sure you book the hotels as 1 or 2 people per room (or whatever arrangement you have). I ALWAYS book my hotel as 1 person except when it has something like breakfast or executive lounge included. But in Japan it was a problem EVERYWHERE. We just caught on and amended bookings. The Japanese are mega rule followers. Every part of the T&C is upheld. Late checkout, theme park ticketing (lol read above) - this is a good and bad thing, but it caught us out a few times. In the US and Europe it tends to be a bit more of a conversation and sometimes you get lucky.
Cash is good for topping up the QC cards above. Other than that, we only needed cash for the express pass and food machines at Spa Land.
Try researching flight prices at flights.google.com. JAL has the best leg room and seat width. I'd say Singapore is next (we did this, via Singapore).
Have fun, I've caught the bug and want to go back already!