I've been to Japan twice, once in 2000 after studying the language and culture for a few years in college, and again this past March. Its a blast, you'll love it!
Seems like you have most things covered, my only real advice is to make sure you pack light if you are using the shinkansen (bullet train). If your luggage is carry-on size or only a bit bigger than that it will make travelling much much easier.
Where are you going besides Tokyo? And when?