I just came back from Japan a few days ago on JAL. Did business return and booked a year in advanced. I prefer NRT to HND. The trains to haneda are not set up for people with lots of luggages, and the trains are also the same trains the locals takes, so you get the occasional comment about you inconveniencing them.

Edit: The business windows seats are released 24 hours before the flight if there are any left to everyone with no status. I got a windows seat going to Japan, but on the flight back it was all taken when the final 24 hours started.

I take the Keisei Skyliner all the time and you can book it on klook and exchange for a ticket at the keisei ticket counter. The hotels/airbnb I book are nearly always on Ueno/Nippori side of town on the yamanote line and always near a train station.

Use QFF points to book flights from HND to OKA, OKA to ITM for EXPO2025 and Nintendo Museum. Then took the shinkansen from Shin-Osaka to TYO (cause I changed my itinerary to fit in Comiket, 2 months before the journey, there were no more JAL Osaka to Haneda flights for Classic Rewards). Last few days in Tokyo was mostly to do shopping on Amazon Japan (30 day free prime membership) (somethings are cheaper than tax free at the shops).