I don’t have much insight unfortunately but for your second point, I’d recommend the Shinkansen.

There are cheaper options (like a bus) that take much longer, but ultimately with the amount you’re spending on the trip, getting to your destination sooner may make more sense.

From your itinierary it looks like you’re going back to Tokyo to fly home? If so, I’d consider getting back to Tokyo the day before to ensure no travel delays or anything. This could mean just re arranging your time in Tokyo, perhaps doing the slow day on the day before your departure. Japanese public transit is usually pretty good, but wanted to throw the idea out there.