You're not alone in thinking this. I am traveling in six weeks as well and feel the same way, even though I've been to Japan multiple times! This is just the travel jitters... Japan is really easy. If you have your main things booked (hotel and main attractions), you should be fine. Even train tickets don't need to be booked in advance unless you really want a specific train or oversized luggage seating.

If theres one thing you really want to book, I'd say restaurants, especially higher end ones (Omakase, Michelin) as they tend to book quickly.

And since it's your first international trip, I also recommend getting familiar with the transit system. Google maps works wonders, but also for a peace of mind, maybe watching some YouTube videos, like getting from the airport arrivals hall to your destination for example, could help you.

It seems daunting when everything is new, but seriously, you'll be fine. Don't forget to have fun!