I agree with all of the suggestions above. I had fear as well going from the US to Tokyo. And, I can tell you, that going to Japan was actually easier than going to most other major US cities. Two or three things to consider:

1. Buy the Fodor Tokyo guide book. I get the print version because you do not need a computer or internet access to reference it. Also, my mom and I put post-it notes into the pages where we were interested. Check out their free site here. http://www.fodors.com/world/asia/japan/
Fodor's have excellent guidebooks that can really organize the information you need for a successful trip and also provide recommendations for different types of tourists (i.e. with kids, adults, adventure seekers).
2. JTB Sunrise tours does offer some very good tours. They have various tours in Tokyo, and these can be quite helpful. I took their tour in Kyoto which was good. I also have friends who did a tour in Tokyo. One of them is an american from Japan, and even he learned from it, so I would recommend it. http://www.jtb-sunrisetours.jp/
3. Watch 'Lost in Translation'. I think it definitely shows a lot of Japan, but also will help to reduce some of the anxiety you may be having, because you can see americans in Japan in a modern-day setting. For me, it had that effect.

I was scared before I went to. Terrified even. However, I had to go for work, which was probably a good thing, because I could not back out. That being said, it was one of the singular best experiences of my life. I would recommend, however, no matter what you do, to practice good planning. The above resources, and guidebooks and having an idea of what you want to do, and what resources you use will take a lot of the stress away so that you can focus on enjoying your trip.