Tokyo has a lot of bilingual signage now, and many of the people speak at least a little English. The cabs have GPS, so as long as you have the address or the name of where you are going, they can get you there. Tokyo is very safe compared to most cities, just take usual precautians for pick pocketers and purse grabbers (recently this has become more of a problem, but still very low compared to most cities).
You will probably see more on a tour, but you can get around Tokyo fine by yourself and do whatever you want when you want. The museum I went to had English translation. The subway was a little confusing, but the people who worked in the subway always helped me when I needed help. The culture is very polite there, people in the service industry will help you. The area of Roppongi in Tokyo has a lot of people from everywhere, and a lot of Americans. There are also restaurants in the area that have been transplanted from America if you need some food you are more accustomed to. Not only a Hard Rock Cafe, but we also got good Mexican food in that area (a little local joint, not a chain). I think Wolfgang Pucks restaurant was there too? Or, nearby.
I would look at tours for ideas about where to go and how to plan the trip. You might consider a very short tour if they are available? 2 or 3 day tour, and then once you feel familiar with the city see more of what you want to see. One part of Tokyo has lots of young people who all dress up funky to go out, I can’t remember the name of the section. They sell hallowee-like clothing all year round for young people who want to dress up. That type of thing might get missed on a tour.