I definitely recommend the JR pass, it's great value if you want to see more than one place. Book it before you go, tourists get a special deal that is unavailable to locals.
Japanese language is a big barrier, yet I found it easier to get around in Japan than in Europe or the USA. That's because the Japanese go out of their way to help you out. Also, most restaurants use pictures or plastic models of the food which really helps a lot.
Having said that, use the free Duolingo app to learn some of the basics of Japanese. Just learning a bit will help a great deal.
Bring lots of nice gifts from your home region for when you meet locals. They will really appreciate it.
As for sights to see, Japan has a lot to offer. I really liked Himeji. The castle and gardens are beautiful!
I'm actually planning another trip to Japan myself this October.
Don't overly worry about your passport. I never lost mine and Japan is exceptionally safe. However, if you do lose it then it's a big pain to replace it, so some simple precautions make sense. I just put (scans of) important documents in a "Travel" directory in my Dropbox folder. That way it's automatically copied to my phone. This is not just for passport but also e.g. hotel reservations, flight bookings, etc. Nice to have it all in one place and impossible to lose, provided you know your dropbox password